Easy synthesis of new series of pteridine analogs: Di- and tetrahydropyrimido[ 4,5-d]pyrimidines via 5-pyrimidinecarbaldehydes

Article abstract of DOI:10.3998/ark.5550190.p008.653

Pyrimidine-5-carbaldehyde derivatives, of easy access, were selected as precursors for the synthesis of mimic pteridine derivatives 5,6- dihydropyrimido[4,5-d]pyrimidines and 5,6,7,8- tetrahydropyrimido[4,5-d] pyrimidines via 4-amino-(5-aminomethyl)pyrimidine intermediates. Straightforward procedures allow a quick access to these compounds. The dihydro derivatives were prepared means of a final cyclocondensation carried out with orthoesters, catalysed by acid and assisted by microwaves irradiation under solvent free conditions. The final cyclocondensation with carbonyl compounds forming the tetrahydro derivatives was done under mild conditions, in which stereochemical induction was carried out on the building of this skeleton, and stereochemistry assignments corroborated by theoretical calculations.ARKAT-USA, Inc.

Full text of DOI:10.3998/ark.5550190.p008.653

General Papers
ARKIVOC 2014 (v) 42-63
Easy synthesis of new series of pteridine analogs: di- and tetra-
hydropyrimido[4,5-d]pyrimidines via 5-pyrimidinecarbaldehydes
José M. de la Torre,a Manuel Nogueras,a Eduardo J. Borkowski,b Fernando D. Suvire,b
Ricardo D. Enriz,b and Justo Cobo*a
a Depto Química Inorgánica y Orgánica, Facultad de Ciencias Experimentales,
Campus las Lagunillas, Universidad de Jaén, E-23071 Jaén, Spain
b Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis,
Chacabuco 915, 5700 San Luis, Argentina
E-mail: jcobo@ujaen.es
In Memoriam: Professor Alan R. Katritzky, for his dedication and contribution
to the world of chemistry
Abstract
Pyrimidine-5-carbaldehyde derivatives, of easy access, were selected as precursors for the
synthesis of mimic pteridine derivatives 5,6-dihydropyrimido[4,5-d]pyrimidines and 5,6,7,8-
tetrahydropyrimido[4,5-d]pyrimidines via 4-amino-(5-aminomethyl)pyrimidine intermediates.
Straightforward procedures allow a quick access to these compounds. The dihydro derivatives
were prepared means of a final cyclocondensation carried out with orthoesters, catalysed by acid
and assisted by microwaves irradiation under solvent free conditions. The final cyclo-
condensation with carbonyl compounds forming the tetrahydro derivatives was done under mild
conditions, in which stereochemical induction was carried out on the building of this skeleton,
and stereochemistry assignments corroborated by theoretical calculations.
Keywords: 4-Amino-5-(aminomethyl)pyrimidines; microwave irradiation; theoretical
calculations; acid catalysis; cyclocondensation; stereoselectivity
Introduction
Pyrimidine-fused compounds are of interest in medicinal chemistry and chemical biology due to
their wide range of biological activities.1-4 See Figure 1 for compounds with the pyrimido[4,5-d]-
pyrimidine scaffold that have been found to show pharmacological activity, such as antiplatelet,5
tyrosine kinase inhibitor,6-8 antifolate (I-II),9 antibacterial (III-IV),10,11 anti-inflammatory,12
hepatoprotective (V)13 and antiviral14 properties.
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Figure 1. Some pyrimido[4,5-d]pyrimidine derivatives with diverse biological properties.
On account of the pharmaceutical interest in these compounds, the development of high-
throughput methodologies for the synthesis of novel pyrimidine-fused heterocyclic scaffolds is in
continuous expansion.15-19 It has become widely accepted that many classical reactions perform
better under microwave irradiation than by conventional heating methods.20-24 Microwave
irradiation has been used to carry out a wide range of reactions in short times, with high yields
and regioselectivity, and frequently without the need of solvents.25
With the aim to tune up simple reaction methodologies, we have focused our strategy in the
use of 4-aminopyrimidine-5-carbaldehydes as key precursors for the preparation of cited fused
heterocyclic system (see Figure 2) because they have the appropriate spatial arrangement of
atoms. We have previously reported some 4-aminopyrimidine-5-carbaldehydes and employed
them for the preparation of pyridopyrimidine derivatives.26
Figure 2
We here present the synthesis of a new series of 5,6-dihydro and 5,6,7,8-tetrahydro
derivatives by a three step process starting from the corresponding 4-aminopyrimidines, via
formation of 4-amino-(5-aminomethyl)pyrimidines as intermediates for further
cyclocondensation with orthoesters and carbonyl compounds respectively.
In the tetrahydropyrimido[4,5-d]pyrimidines a stereogenic center is generated and the
experimental conditions to induce stereoselectivity are discussed below.
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Results and Discussion
The key precursor 6-aminopyrimidin-4(3H)-one-5-carbaldehydes, 1a,b, were prepared by
Vilsmeier-Haack formylation of 6-aminopyrimidin-4(3H)-ones VI,26 and then reaction with
various primary amines, such as aniline, benzylamine and cyclohexylamine, in order to get the
required diamino intermediate 2 for further cyclocondensation via reaction with the carbaldehyde
group. The standard reductive reagents and conditions were tested in order to afford compounds
2, but just the use of sodium triacetoxyborohydride in THF was effective to perform the one step
amino reduction. The reaction workup is simple and straightforward, and compounds 2 were
isolated by filtration in good to excellent yields (Scheme 1 and Table 1).
Scheme 1. Synthetic route to pyrimidopyrimidines 3 from aminopyrimidines.
Table 1. Data for the synthesis of 2a-g shown in Scheme 1
Compounds 2
Entry
X
R1
Yield (%)
Mp ºC
250
125
210
175
118
140
-
O
O
O
S
C6H5
CH2C6H5
C6H11
98
82
2a
2b
80
2c
C6H5
92
2d
S
CH2C6H5
C6H11
78
2e
S
90
2f
S
CH(CH3)C6H5
86/81
2g/g′
Compounds 2 were fully characterized by spectroscopic and analytical data. From the
spectroscopic data of compounds 2, the disappearance of signals corresponding to the
carbaldehyde in 1, and the appearance of the derived methylene group and the signals which
correspond to the amine residue, are clearly observed. In the case of 2a, the signal for 5-CH2 is
observed at 3.95 ppm (as a doublet, coupled with NH) and at 37.0 ppm, in the 1H- and 13C-NMR
spectra respectively.
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For the cyclocondensation of the diamine derivative 2, we first tried several acid derivatives
such as acyl chlorides and anhydrides, and different conditions, but with no positive results.
Finally we chose orthoesters, which provided the corresponding 5,6-dihydropyrimido[4,5-d]-
pyrimidin-4(3H)-ones 3, in satisfactory yields.
According to the literature, reactions with this kind of reagent need drastic conditions.27,28 An
attempt to carry out these reactions by conventional heating gave decomposition of starting
material because of the long reaction times required. To avoid conventional heating, we chose to
assist the reaction with microwave irradiation, and we found that the reaction took place at 200
ºC over 10–15 minutes with orthoester in excess (three- and four-fold molar) and in the absence
of solvent to yield the desired pyrimidopyrimidines 3, but not in good yields (< 45 %). This was
probably due to the partial decomposition of the products under such conditions. From the
different acid catalysts screened to optimize the reaction conditions, acetic acid was found to
give the best results. After addition of acetic acid the reactions were greatly improved: the
reaction time fell to 1 minute, the temperature for the reaction dropped to 150 ºC, and yields
were considerably increased (Table 2). Nevertheless no useful results were obtained when the 6-
amino-5-(phenylaminomethyl)pyrimidin-4-one 2a was taken as starting material.
Table 2. Data for the reaction of 2 with orthoesters to products 3a-i with AcOH as catalyst (see
Scheme 1)
Compounds 3
Entry
X
R1
R2
Yield (%)
Mp ºC
178
142
227
174
146
126
115
189
237
O
O
O
S
S
S
S
S
S
CH2C6H5
CH2C6H5
C6H11
H
CH3
H
65
49
80
75
60
70
67
69
53
3a
3b
3c
3d
3e
3f
C6H5
H
C6H5
CH3
H
CH2C6H5
CH2C6H5
C6H11
CH3
H
3g
3h
3i
C6H11
CH3
Compounds 3 were fully characterized by spectroscopic and analytical data. From
spectroscopic data of compounds 3, the formation of the new pyrimidine ring is clearly observed:
in the 1H-NMR spectra the signals for NH are absent and instead the proton or methyl attached to
C(7) appears at 7.40-8.12 ppm or around 2.0 ppm respectively; in the 13C-NMR the C(7) appears
at 152-164 ppm.
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In the hope of improving the reaction efficiency, equimolar amounts of 6-amino-5-
(benzylaminomethyl)pyrimidine 2b, ethyl orthoformate and acetic acid were tried; but in this
case in addition to the cyclization reaction we found loss of the methoxy group at C(2), clearly
1
indicated in the H-NMR in which the NH of the lactam moiety was found (broad singlet at
10.90 ppm) for 3j (Scheme 2). Something similar has been reported in other acid reactions in the
presence of a nucleophile such as ethanol, which is a byproduct of the cyclocondensation
step.26,29
Scheme 2. Acetic acid in equimolar amount leads to demethylation and cyclization in the
reaction of diaminopyrimidine 2b with ethyl orthoformate.
All the pyrimidopyrimidines 3 were fully characterized, the most characteristic NMR feature
being the afore-mentioned disappearance of the NH signals of 2 and the appearance of a new
signal for C(7)-H in the case of 3a,c,d,f,h or -CH3 for 3b,e,g,i depending on whether ethyl
orthoformate or methyl orthoacetate were used.
X-Ray diffraction analysis was carried out on the pyrimido[4,5-d]pyrimidine 3a, and its
structure was unambiguously confirmed. The most relevant feature observed in its supra-
molecular structure is the π – π stacking interactions between phenyls which is reinforced by
weak π – π interactions between pyrimidine rings.
Figure 3. ORTEP drawing of the structure 3a with 50% probability ellipsoids.
In order to extend the variety of hydropyrimido[4,5-d]pyrimidines available, the tetrahydro
derivatives were prepared from the intermediates 2 and carbonyl compounds such as acetone and
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benzaldehyde in a similar fashion to those reported for the preparation of tetrahydroquin-
azolines.30 Mild reaction conditions were used: EtOH as solvent, a temperature of 50 ºC, and
p-toluenesulfonic acid as catalyst, which is needed because of the low nucleophilicity of the 6-
amino group in 2 (Scheme 3 and Table 3).31
Scheme 3. Synthesis of 5,6,7,8-tetrahydropyrimido[4,5-d]pyrimidin-4(3H)-ones 4.
Table 3. Data for products 4a-g
Compounds 3
Entry
X
R1
R2
R3
Yield (%)
Mp ºC
222
220
169
156
261
126
115
O
S
CH2C6H5
CH2C6H5
CH2C6H5
CH2C6H5
C6H11
CH3
CH3
H
CH3
CH3
C6H5
C6H5
H
70
74
4a
4b
4c
O
S
72
H
55
4d
4e a
4f
O
S
H
40
C6H11
H
C6H5
67
38-72 b
S
CH(CH3)C6H5
H
C6H5
4g
a Compound 4e was isolated from the reaction of 2c with acetone.b See Table 4.
The tetrahydropyrimidopyrimidines 4 were obtained in moderate to good yields and also
fully characterized by spectroscopic and analytical data. From the spectroscopic data of
compounds 4, the formation of the new tetrahydropyrimidine ring is clearly observed, for
1
example in H-NMR spectra; as in the case of compounds 3, the signals for NH largely
disappear, there remaining just the N(8)-H, and substituents attached to C(7) are clearly
observed, with the new C(7) appearing in the 13C-NMR at 59-71 ppm.
The reaction between 2c and acetone afforded an unexpected product, which was
1
characterized as 4e. Its H-NMR spectrum shows a signal at 4.78 ppm corresponding to the
methylene for C(7), which is coupled with the N(8)-H, but not those corresponding to the methyl
groups expected from acetone. So the acetone is not involved in the reaction in this case, as was
also confirmed by mass spectrometry. To prove this possibility 2c was reacted in ethanol with
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PTSA in the absence of acetone. Under these conditions compound 4e, together with the initial
pyrimidine precursor VI and cyclohexylamine were obtained. Therefore, compound 2c is acting
in this reaction both as a diamine and a formaldehyde-releasing agent, to render 4e, as shown in
Scheme 4. This behavior can be explained by of the higher basicity of the dialkylamino residue
in molecule 2c, compared to the other diamine derivatives 2, that in acid media leads to its partial
hydrolysis that releases formaldehyde (like in acetals) which is then trapped by another molecule
of 2c, forming compound 4e.
Scheme 4. Compound 2c: decomposition in acid medium.
From the mass spectrometry analysis for the dihydro (3) and tetrahydro (4) pyrimido[4,5-d]-
pyrimidine derivatives, similar fragmentation patterns were observed, characterized by
progressive loss of pendant substituents and ring opening.
A single crystal X-ray diffraction on the tetrahydropyrimido[4,5-d]pyrimidine derivative 4c
was carried out (Figure 4), showing the predicted structure. Some considerations about the
structure observed can be made: the puckering analysis shows a conformation of the saturated 6-
membered ring close to the twist-boat, with substituents at N(6) and C(7) in a axial disposition to
minimize the steric interaction between them.
Figure 4. ORTEP drawing of the structure 4c with 50% probability ellipsoids.
When benzaldehyde is used as reagent, a stereogenic center is generated at C(7) (see Figure
5). In the first instance we observed that in order to induce stereoselectivity in this reaction, the
presence of a chiral residue in the starting material was needed, and therefore the enantiomeric
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compounds 2g/2g’ were prepared by reductive amination of 1b with (R)- and (S)-
methylbenzylamine. The stereoselectivity of the reaction of 2g/2g’ with benzaldehyde was
studied under several conditions. The conclusions of the chirality study are: slight importance of
solvent (better results in acetonitrile than in ethanol), the necessity for a chiral auxiliary
introduced in the molecule (R1) (2g/2g’) and also a chiral acid catalyst (camphorsulfonic acid).
Without chiral acid catalyst the d.e. of the reaction was 4% in EtOH and 33% in acetonitrile,
while it reaches 88% upon the addition of camphorsulfonic acid (Table 4). When the substituent
is the isomer S and the acid is S too, the preferred configuration generated is S. Likewise, when
starting material and catalyst are R, C(7) is also R, and in both cases the diastereomeric excess
obtained is around 88% (see Table 4).
Figure 5. Set of diasteromeric structures formed by reaction of 2g/2g′ with benzaldehyde.
Table 4. Results of the stereochemical analysis of the chiral diaminopyrimidines 2g/2g′
Major
isomer
Starting chiral
diamine (2)
Yield
(%)
Conditions
d.e [α(D)]
4% [+16.6º]
33 %
2g [1′R (+)]
EtOH, refl. / PTSA·H2O (10%)
38
4g1
CH3CN, 50 ºC / PTSA·H2O
(10%)
2g [1′R (+)]
44
4g1
2g [1′R (+)]
2g [1′R (+)]
2g [1′R (+)]
EtOH, 50 ºC / CSA (+) (10%)
86 %
72
66
72
4g1
4g1
4g1
CH3CN, 50 ºC / CSA (+) (10%) 88 % [+84.4º]
CH3CN, 50 ºC / CSA (-) (10%)
78 %
58 %
EtOH, 50 ºC / PTSA·H2O
(10%)
4g4
2g′ [1′S (-)]
72
2g′ [1′S (-)]
2g′ [1′S (-)]
CH3CN, 50 ºC / CSA (+) (10%)
CH3CN, 50 ºC / CSA (-) (10%)
50 %
56
68
4g4
4g4
82 % [-77.2º]
Analysis by NMR was essential to determine the stereochemistry in the 4g diasteromers and
to calculate the diasteromeric excess for the reactions. NOESY experiments permitted
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assignment of 4g1 as the major diastereoisomer (see figures 1S and 2S in supporting
information). The NOESY (figure 1S) shows the correlation between C(7)-H with 1′-H for 4g1,
but in the case of 4g2 are observed between C(7)-H with 1′-CH3 and N(8)-H with 1′-H, which
agrees with their optimized conformations.
Theoretical calculations
To support the experimental results, theoretical calculations have been done on compound 4g1-4.
An exhaustive conformational study has been carried out using the Multidimensional
Conformational Analysis (MDCA).32 A combination of semiempirical (PM6) and DFT
(B3LYP/6-31G(d)) computations were employed in order to obtain the energetically preferred
conformations. A detailed explanation about the conformational search is given in the
experimental section. From the low-energy conformations obtained for both diasteromers R/R
and R/S we calculated the shielding tensors using the GIAO approach33,34 from the program
Gaussian 03.35 Our study also includes the calculation of 13C-NMR chemical shift for the
diasteroisomers (R/R; R/S; S/R and S/S) by using the gauge independent atomic orbital (GIAO)
approximation.
Observing the curves obtained in figure 6, it is evident that the correlation obtained for the
R/R enantiomer is excellent indicating that such assignment for 4a-g is correct. Figures 6a and 6b
give the correlations obtained for the experimentally obtained chemical shifts versus calculated
chemical shifts obtained for R/R and R/S, respectively.
a)
b)
R/R exp
R/R exp
R/R Cal
R/S Cal
Figure 6. Chemical shifts correlations: (a) assigned to R/R vs calculated for R/R, and (b)
assigned to R/R vs calculated for R/S
It is pertinent to remark that the theoretical calculations reported here are in agreement with
the experimental results obtained from X-ray measurements. Figure 3S (supporting information)
gives in a comparative fashion the conformations obtained from X-ray and from theoretical
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calculations. The very similar spatial ordering obtained for both forms can be appreciated very
well in this figure.
Antimicrobial activity
It should be noted that the synthesized compounds have a certain structural similarity with
compounds IV and V shown in Figure 1 which have been reported as antibacterial agents Thus,
we decide to test these compounds against different pathogenic fungi and bacteria. Minimum
Inhibitory Concentration (MIC) of each compound was determined by using broth microdilution
techniques according to the guidelines of the National Committee for Clinical Laboratory
Standards for yeasts (M27-A3) and for filamentous fungi (M 38-A2).36 More details about these
bioassays might be obtained from previous works.37-38
Most of the compounds described herein were evaluated against Candida albicans, C.
neoformans, Staphylococcus aureus methicillin-sensitive ATCC 29213, Staphylococcus aureus
methicillin-resistant ATCC 43300, Escherichia coli ATCC 25922, LM1-Escherichia coli LM2,,
Pseudomonas aeruginosa ATCC 27853, PI-Yersinia enterocolítica, MI-Salmonella enteritidis
and Salmonella sp (LM). Unfortunately, none of the test compounds displayed antifungal nor
antibacterial activity at the highest concentration tested (250 ꢀg/mL). Other bioassays are in
progress and will be the subject of another report in the near future.
Conclusions
We have developed the synthesis of a new series of 5,6-dihydro- and 5,6,7,8-
tetrahydropyrimido[4,5-d]pyrimidin-4(3H)-ones starting from the corresponding 4-amino-
pyrimidines, via formation of 4-amino-(5-aminomethyl)pyrimidines as intermediates. The
cyclocondensation was achieved using orthoesters under MW irradiation and solvent-free
conditions. This latter reaction was optimized by acid catalyst to get the desired products in just
1 minute in good yields. This methodology is straightforward and the isolation of desired
products is simple. These compounds have an attractive skeleton from a biological point of view,
and they are being tested with the aim to find potential pharmacological applications.
Experimental Section
General. Melting points were determined on a Barstead Electrothermal 9100 melting point
apparatus. IR spectra were recorded in KBr disks on a Bruker TENSOR 27 spectrophotometer at
1
“Centro de Instrumentación Científico-Técnica (CICT) at Universidad de Jaén”. H and 13C
NMR spectra were recorded on a Bruker Avance 400 spectrophotometer (CICT) operating at 400
MHz and 100 MHz respectively, using CDCl3 and DMSO-d6 as solvents and tetramethylsilane as
internal standard; the carbon type described p (primary), s (secondary), t (tertiary) and q
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(quaternary) at 13C-NMR was done using DEPT-135 and 2D-NMR experiments. Mass spectra
were run on a Shimadzu-GCMS 2010-DI-2010 spectrometer (equipped with a direct inlet probe)
operating at 70 eV. High resolution mass spectra were run on a Waters Micromass AutoSpec-
Ultima spectrometer equipped with a direct inlet probe operating at 70 eV. Silica gel aluminum
plates (Merck 60 F254) were used for analytical TLC. The microwave-assisted reactions were
carried out in a 10 ml glass sealed vial for focused mono-mode microwaves oven (Discover, by
CEM Corp.) working in standard mode by controlling the target temperature. The starting
amines and orthoesters were purchased from Aldrich, Fluka and Acros (analytical reagent
grades) and were used without further purification.
Reductive amination of 6-aminopyrimidine-5-carbaldehydes (1): 6-amino-5-[(substituted-
amino)methyl]pyrimidin-4(3H)-ones (2). General procedure. The 6-aminopyrimidine-5-
carbaldehyde (1) (1 mmol) was suspended in anhydrous THF under argon. The requisite primary
amine (2 mmol) and then sodium triacetoxyborohydride (2 mmol) were added and stirred was
continued overnight at room temperature. The solvent was removed under reduced pressure and
water (20 mL) was added. The solution was neutralized with aqueous sodium hydroxide (2 M).
The desired colorless product (2) was precipitated, filtered off, and washed with water.
6-Amino-2-methoxy-3-methyl-5-[(phenylamino)methyl]pyrimidin-4(3H)-one (2a) from 1a
and aniline, yield 98 %. Mp 250-3 ºC. IR (KBr): 3358 (b,m); 3182 (m); 2953 (w); 1644 (b,s);
1
1541 (b,s); 1485 (m); 1452 (m); 1411 (m); 1216 (m). H-NMR (DMSO-d6) δ (ppm): 3.19 (s,
3H); 3.87 (s, 3H); 3.94 (d, 5.4 Hz, 2H); 5.47 (t, 5.4 Hz, 1H); 6.35 (s, 2H); 6.46 (t, 7.2 Hz, 1H);
6.61 (d, 7.2 Hz, 2H); 7.00 (t, 7.2 Hz, 2H). 13C-NMR (DMSO-d6) δ (ppm): 27.0 p; 37.1 s; 55.0 p;
87.9 q; 112.3 t; 115.3 t; 128.6 t; 148.7 q; 155.1 q; 159.4 q; 162.0 q. MS (70 eV) m/z (%): 260
(M+, 10); 257 (23); 168 (100); 111 (10); 93 (3); 77 (5). HRMS (EI, 70 eV): calc for C13H14N4O2
260.1273; found 260.1270.
6-Amino-5-[(benzylamino)methyl]-2-methoxy-3-methylpyrimidin-4(3H)-one (2b) from 1a
and benzylamine, yield 82 %. Mp 125-7 ºC. IR (KBr): 3360 (m); 3311 (m); 3200 (b,m); 2952
1
(w); 2853 (w); 1623 (b,s); 1540 (b,s); 1487 (m); 1221 (m). H-NMR (DMSO-d6) δ (ppm): 3.16
(s, 3H), 3.52 (s, 2H), 3.60 (s, 2H); 3.88 (s, 3H); 6.47 (s, 2H); 7.17 – 7.24 (m, 2H); 7.25 – 7.30
13
(m, 4H). C-NMR (DMSO-d6) δ (ppm): 26.9 p; 42.9 s; 52.0 s; 55.0 p; 88.1 q; 127.4 t; 127.9 t;
128.0 t; 141.0 q; 155.0 q; 159.7 q; 161.9 q. MS (70 eV) m/z (%): 272 (M+, 4); 183 (100); 169
(83); 91 (30). HRMS (IE, 70 eV): calc for C14H16N4O2 272.1273; found 272.1271.
6-Amino-5-[(cyclohexylamino)methyl]-2-methoxy-3-methylpyrimidin-4(3H)-one (2c) from
1a and cyclohexylamine, yield 80 %. Mp 210-2 ºC. IR (KBr): 3371 (s); 3296 (m); 3182 (b,m);
1
2920 (m); 2853 (m); 1635 (b,s); 1598 (m); 1546 (b,s); 1452 (s). H-NMR (DMSO-d6) δ
(ppm):0.94 – 1.02 (m, 2H); 1.08 – 1.18 (m, 3H); 1.48 – 1.52 (m, 1H); 1.61 – 1.63 (m, 2H); 1.79 –
1.82 (m, 2H); 2.26 – 2.31 (m, 1H); 3.15 (s, 3H); 3.50 (s, 2H); 3.87 (s, 3H); 6.49 (s, 2H). 13C-
NMR (DMSO-d6) δ (ppm): 24.4 s; 25.9 s; 26.9 p; 32.8 s; 40.3 s; 54.8 t; 54.9 p; 88.5 q; 154.9 q;
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159.7 q; 161.7 q. MS (70 eV) m/z (%): 183 (100); 168 (61); 111 (13); 98 (20); 56 (22). HRMS
(IE, 70 eV): calc for C13H20N4O2 264.1586; found 264.1588.
6-Amino-3-methyl-2-(methylthio)-5-[(phenylamino)methyl]pyrimidin-4(3H)-one (2d) from
1b and aniline, yield 92 %. Mp 175-7 ºC. IR (KBr): 3486 (m); 3386 (s); 3298 (m); 2922 (w);
1
2844 (w); 1600 (b,s); 1524 (b,s); 1317 (m); 1093 (m). H-NMR (DMSO-d6) δ (ppm): 2.48 (s,
3H); 3.31 (s, 3H); 3.96 (d, 5.6 Hz, 2H); 5.51 (t, 5.6 Hz, 1H); 6.40 (sa, 2H); 6.47 (pt, 6.4 Hz, 1H);
6.61 (pd, 6.4 Hz, 2H); 7.00 (pt, 7.2 Hz, 2H). 13C-NMR (DMSO-d6) δ (ppm): 14.1 p; 29.5 p; 37.0
s; 89.8 q; 112.4 t; 115.4 t; 128.7 t; 148.6 q; 158.7 q; 159.8; 161.5 q. MS (70 eV) m/z (%): 276
(M+, 10); 184 (100); 138 (5); 93 (15). HRMS: calc for C13H16N4OS 276.1045; found 276.1047.
6-Amino-5-[(benzylamino)methyl]-3-methyl-2-(methylthio)pyrimidin-4(3H)-one (2e) from
1b and benzylamine (0.22 ml) (78 %). M. p. 118-21 ºC. IR (KBr): 3381 (m); 3284 (m); 2922
1
(w); 2859 (w); 1605 (b,s); 1513 (s); 1459 (m); 1411 (m); 1089 (m). H-NMR (DMSO-d6) δ
(ppm): 2.45 (s, 3H); 3.24 (s, 3H); 3.50 (s, 2H); 3.56 (s, 2H); 6.49 (sa, 2H); 7.10 – 7.20 (m, 1H);
7.20 – 7.30 (m, 4H). 13C-NMR (DMSO-d6) δ (ppm): 14.1 p; 29.4 p; 42.8 s; 52.1 s; 90.1 q; 126.5
t; 127.9 t; 128.1 t; 140.9 q; 159.2 q; 159.6 q; 161.5 q. MS (70 eV) m/z (%): 288 (8); 199 (100);
185 (68); 138 (15); 91 (17). HRMS: calc for C14H18N4OS 288.1045; found 288.1039.
6-Amino-5-[(cyclohexylamino)methyl]-3-methyl-2-(methylthio)pyrimidin-4(3H)-one
(2f)
from 1b and cyclohexylamine (0.2 ml) (90 %). IR (KBr): 3380 (s); 3184 (b,m); 2918 (m); 2850
1
(m); 1607 (b,s); 1576 (m); 1521 (s); 1410 (m); 1095 (m). Mp 140-2 ºC. H-NMR (DMSO-d6) δ
(ppm): 0.96 – 1.03 (m, 2H); 1.09 – 1.22 (m, 3H); 1.50 – 1.54 (m, 3H); 1.80 – 1.83 (m, 2H); 2.26
13
– 2.31 (m, 1H); 2.50 (s, 3H); 3.28 (s, 3H); 3.53 (s, 2H); 6.53 (sa, 2H). C-NMR (DMSO-d6) δ
(ppm): 14.0 p; 24.4 s; 25.9 s; 29.3 p; 32.9 s; 40.2 s; 54.8 t; 90.6 q; 159.1 q; 159.2 q; 161.2 q. MS
(70 eV) m/z (%):199 (100); 184 (64); 138 (11); 98 (28); 56 (21). HRMS: calc for C13H22N4OS
282.1514; found 282.1507.
(R)-6-Amino-3-methyl-2-methylthio-5-[[(1-phenylethyl)amino]methyl]pyrimidin-4(3H)-one
(2g) from 1b and
D(+)-α-methylbenzylamine. The product was extracted with DCM (3 × 20
mL). The organic extracts were dried over anhydrous Na2SO4, and solvents removed under
reduced pressure to afford an oily residue. The product was purified by flash chromatography
(eluent DCM/MeOH 9:1;column diam. 2cm) to give a colorless oil (86%). [α]D + 75.8 (DCM; 25
ºC; 0.01g/L). IR (KBr): 3442 (m, b); 2959 (w); 2924 (m); 2852 (w); 1630 (s, b); 1516 (s, b);
1
1452 (m); 1412 (m); 1095 (m, b). H-NMR (DMSO-d6) δ (ppm): 1.41 (d, 6.6 Hz, 3H); 2.49 (s,
3H); 3.41 (s, 3H); 3.47 (d, 13.2 Hz, 1H), 3.74 (d, 13.2 Hz, 1H); 3.84 (q, 6.6 Hz, 1H); 5.45 (sa,
2H); 7.24 –7.27 (m, 1H); 7.31 – 7.37 (m, 4H). 13C-NMR (DMSO-d6) δ (ppm): 14.6 p: 23.5 p;
30.0 p; 42.1 s; 58.2 t; 91.8 q; 126.7 t;127.3 t; 128.6 t; 144.6 q; 159.6 q; 160.8 q; 162.5 q. MS (70
eV) m/z (%):211 (47); 199 (100); 184 (48); 138 (8); 120 (74); 105 (25); 88 (15). HRMS: calc for
C15H20N4OS: 316.1358; found 316.1356.
(S)-6-Amino-3-methyl-2-methylthio-5-[[(1-phenylethyl)amino]methyl]pyrimidin-4(3H)-one
(2g′) from 1b (1 mmol) and L(-)-α-methylbenzylamine. The workup as for 2g gave a colorless
oil (81%). [α]D -74.4 (DCM; 25 ºC; 0.01g/L). NMR and IR are the same as for 2g. MS (70 eV)
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m/z (%): 211 (4547); 199 (100); 184 (5348); 138 (8); 120 (7374); 105 (25); 88 (1315).. HRMS:
calc for C15H20N4OS: 316.1358; found 316.1355.
Synthesis of pyrimido[4,5-d]pyrimidines (3) by cyclocondensation of 2 with orthoesters:
general procedure. A mixture of 6-amino-5-aminomethylpyrimidine (2) (1 mmol), the
orthoester (0.5 ml) and acetic acid (one drop) was placed into a sealed MW glass tube and
irradiated in the microwave oven for 1 minute (150 ºC, max. power 200W). After cooling,
hexane was added and the solid that separated was filtered off, washed with cold diethyl ether,
and recrystallized from ethanol.
6-Benzyl-2-methoxy-3-methyl-5,6-dihydropyrimido[4,5-d]pyrimidin-4(3H)-one (3a) from 2b
and triethyl orthoformate: colorless solid (65 %). Mp 175-82 ºC. IR (KBr): 2955 (b,w); 1705
1
(m); 1654 (b,s); 1556 (b,m); 1496 (m); 1455 (m); 1436 (m); 1212 (m); 1156 (m). H-NMR
(CDCl3) δ (ppm): 3.33 (s, 3H); 4.03 (s, 3H); 4,23 (s, 2H); 4.33 (s, 2H); 7.28 (pd, 7.0 Hz, 2H);
7.33 – 7.41 (m, 3H); 7.40 (s, 1H). 13C-NMR (CDCl3) δ (ppm): 27.6 p; 43.3 s; 55.8 p; 57.4 s; 91.5
q; 127.9 t; 128.5 t; 129.0 t; 133. 5 q; 155.9 t; 156.5 q; 157.9 q; 161.6 q. MS (70 eV) m/z (%): 284
(M+, 5); 193 (20); 182 (13); 168 (20); 133 (17); 106 (35); 91 (100); 75 (31); 65 (37). HRMS: calc
for C15H16N4O2 284.1273; found 284.1271.
Crystal data for 3a were deposited at CCDC with reference 809643: Chemical formula
C15H16N4O2, Mr 284.32, Orthorombic, Pbca, 120 K, cell dimensions a, b, c (Å) 17.948 (5),
7.8393 (15), 18.8278 (13); α, β, γ (°) 90, 90, 90, V (Å3) 2649.1 (9), Z= 8, F(000)=1200, Dx (Mg
m-3) = 1.426, Mo Kα, ꢀ (mm-1)=0.10, Crystal size (mm)= 0.3 × 0.24 × 0.22. Data collection:
Diffractometer KappaCCD diffractometer, Monochromator graphite, CCD rotation images, thick
slices φ & θ scans, absorption correction SADABS 2.10, Tmin, Tmax 0.971, 0.979. No. of measured,
independent and observed [I > 2σ(I)] reflections 23485, 3043, 2071, Rint=0.064, θ values (°): θmax
= 27.5, θmin = 3.1; Range h = -23→23, k = -10→8, l = -22→24, Refinement on F2:R[F2 >
2σ(F2)]=0.048, wR(F2)=0.128, S=1.09. No. of reflections 3043, No. of parameters 192, No. of
2
2
restraints 0. Weighting scheme: w = 1/[σ2(Fo ) + (0.0505P)2 + 1.7324P] where P = (Fo
+
2Fc2)/3. (ꢁ/σ)max=0.001, ꢁσmax, ꢁσmin (e Å-3) 0.31, -0.34.
6-Benzyl-2-methoxy-3,7-dimethyl-5,6-dihydropyrimido[4,5-d]pyrimidin-4(3H)-one
(3b)
from 2b and trimethyl orthoacetate: yellow solid (49 %). Mp 142-3 ºC. IR (KBr): 3006 (w); 2955
(b,w); 2861 (b,w); 2811 (w); 1736 (w); 1666 (s); 1599 (m); 1558 (s); 1533 (s); 1471 (b,s); 1430
(m); 1412 (m). 1H-NMR (CDCl3) δ (ppm): 2.29 (s, 3H); 3.34 (s, 3H); 4.05 (s, 3H); 4.34 (s, 2H);
4.51 (s, 2H); 7.24-7.39 (m, 5H). 13C-NMR (CDCl3) δ (ppm): 22.5 p; 27.6 p; 46.2 s; 54.8 s; 55.8
p; 91.5 q; 126.6 t; 128.1 t; 129.1 t; 134.1 q; 156.6 q; 158.0 q; 161.4 q; 164.2 q. MS (70 eV) m/z
(%): 298 (M+, 2); 207 (27); 91 (100). HRMS: calc for C16H18N4O2 298.1430; found 298.1429.
6-Cyclohexyl-2-methoxy-3-methyl-5,6-dihydropyrimido[4,5-d]pyrimidin-4(3H)-one
(3c)
from 2c and triethyl orthoformate: colorless solid (80 %). Mp 226-8 ºC. IR (KBr): 3177 (m);
1
2932 (m); 2856 (w); 1635 (b,s); 1548 (b,s); 1487 (m); 1455 (m); 1410 (m); 1377 (m). H-NMR
(CDCl3) δ (ppm): 1.15-1.24 (m, 1H); 1.32-1.41 (m, 2H); 1.57-1.66 (m, 2H); 1.72 (pd, 13.8 Hz,
1H); 1.93 (pd, 10.7 Hz, 4H); 3.31-3.38 (m, 1H); 3.38 (s, 3H); 4.05 (s, 3H); 4.44 (s, 2H); 8.12 (s,
1H). 13C-NMR (CDCl3) δ (ppm): 24.8 s; 25.1 s; 27.9 p; 30.1 s; 41.4 s; 56.4 p; 64.4 t; 90.3 q;
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153.0 q; 154.1 t; 157.2 q; 161.1 q. MS (70 eV) m/z (%): 276 (M+, 55); 275 (71); 261 (22); 193
(100); 179 (24); 136 (17); 83 (4). HRMS: calc for C14H20N4O2 276.1586; found 276.1589.
3-Methyl-2-(methylthio)-6-phenyl-5,6-dihydropyrimido[4,5-d]pyrimidin-4(3H)-one
(3d)
from 2d and triethyl orthoformate. Colorless solid (75 %). Mp 173-5 ºC. IR (KBr): 3063 (w);
2924 (w); 2854 (w); 1655 (b,s); 1594 (m); 1547 (m); 1516 (s); 1437 (m); 1405 (b,m); 1225 (m).
1H-NMR (CDCl3) δ (ppm): 2.64 (s, 3H); 3.51 (s, 3H); 4.85 (s, 2H); 7.24-7.31 (m, 3H); 7.45 (pt,
7.4 Hz, 2H); 7.79 (s, 1H). 13C-NMR (CDCl3) δ (ppm): 15.0 p; 30.1 p; 44.2 s; 94.4 q; 119.2 t;
126.4 t; 129.8 t; 142.0 q; 153.2 t; 156.5 q; 160.9 q; 162.6 q. MS (70 eV) m/z (%): 286/288
(M/M+2, 66/13); 271 (47); 198 (24); 77 (100). HRMS: calc for C14H14N4OS 286.0888; found
286.0891.
3,7-Dimethyl-2-(methylthio)-6-phenyl-5,6-dihydropyrimido[4,5-d]pyrimidin-4(3H)-one (3e)
from 2d and trimethyl orthoacetate: yellow solid (60 %). Mp 145-8 ºC. IR (KBr): 3039 (w); 2928
1
(w); 1724 (m); 1645 (b,s); 1513 (b,s); 1477 (m); 1448 (b,m); 1410 (m); 1342 (m). H-NMR
(DMSO-d6) δ (ppm): 1.81 (s, 3H); 2.50 (s, 3H); 3.34 (s, 3H); 4.54 (s, 2H); 7.35-7.41 (m, 1H);
7.44-7.51 (m, 4H). 13C-NMR (DMSO-d6) δ (ppm): 14.4 p; 23.0 p; 29.6 p; 48.8 s; 93.2 q; 126.3 t;
128.0 t; 129.9 t; 143.3 q; 157.1 q; 159.5 q; 161.0 q; 162.8 q. MS (70 eV) m/z (%): 300 (M+, 62);
299 (100); 285 (42); 77 (27). HRMS: calc for C15H16N4OS 300.1045; found 300.1044.
6-Benzyl-3-methyl-2-(methylthio)-5,6-dihydropyrimido[4,5-d]pyrimidin-4(3H)-one
(3f)
from 2e and triethyl orthoformate: colorless solid (70 %). Mp 126 ºC. IR (KBr): 2996 (w); 2931
1
(w); 1701 (s); 1661 (b,s); 1560 (s); 1519 (s); 1461 (m); 1428 (s); 1367 (b,s); 1284 (b,m). H-
NMR (CDCl3) δppm: 2.61 (s, 3H); 3.43 (s, 3H); 4.25 (s, 2H); 4.33 (s, 2H); 7.27-7.38 (m, 5H);
13
7.41 (s, 1H). C-NMR (CDCl3) δ (ppm): 15.0 p; 29.9 p; 43.1 s; 57.5 s; 93.5 q; 127.9 t; 128.6 t;
129.1 t; 133.4 q; 156.0 t; 157.4 q; 161.1 q; 162.1 q. MS (70 eV) m/z (%): 300 (M+, 4); 209 (33);
91 (100). HR MS: calc for C15H16N4OS 300.1045; found 300.1042.
6-Benzyl-3,7-dimethyl-2-(methylthio)-5,6-dihydropyrimido[4,5-d]pyrimidin-4(3H)-one (3g)
1
from 2e and trimethyl orthoacetate: yellow solid (67 %). Mp 114-16 ºC. H-NMR (CDCl3) δ
(ppm): 2.30 (s, 3H); 2.63 (s, 3H); 3.44 (s, 3H); 4.36 (s, 2H); 4.51 (s, 2H); 7.24-7.39 (m, 5H). 13C-
NMR (CDCl3) δ (ppm): 14.9 p; 22.6 p; 29.6 p; 46.0 s; 54.8 s; 93.5 c, 126.6 t; 128.1 t; 129.1 t;
134.0 q; 157.6 q; 160.8 q; 162.0 q; 164.3 q. IR (KBr): 2999 (w); 2927 (w); 2841 (w); 1720 (w);
1650 (b,s); 1519 (b,s); 1484 (m); 1453 (m); 1408 (m). MS (70 eV) m/z (%): 314/316 (M/M+2,
4/1); 223 (37); 91 (100). HR MS: calc for C16H18N4OS 314.1197; found 314.1201.
6-Cyclohexyl-3-methyl-2-(methylthio)-5,6-dihydropyrimido[4,5-d]pyrimidin-4(3H)-one (3h)
from 2f and triethyl orthoformate: colorless solid (69 %). Mp 187-91 ºC. IR (KBr): 2934 (w);
2856 (m); 1709 (m); 1650 (b,s); 1591 (m); 1520 (b,s); 1460 (m); 1412 (m). 1H-NMR (CDCl3) δ
(ppm): 1.15 (tq, 3.7 y 13.0 Hz, 1H); 1.35 (qt, 3.7, 13.0 Hz, 2H); 1.60 (qd, 3.5 Hz y 12.0 Hz, 2H);
1.70 (pd, 13.7 Hz, 1H); 1.89 (pt, 13.2 Hz, 4H); 2.60 (s, 3H); 3.20 (tt, 3.3 Hz y 12.0 Hz, 1H); 3.47
(s, 3H); 4.43 (s, 2H); 7.65 (s, 1H). 13C-NMR (CDCl3) δ (ppm): 15.0 p; 24.9 s; 25.2 s; 30.0 p; 30.1
s; 63.4 t; 92.6 q; 154.8 t; 155.6 q; 160.8 q; 162.8 q. MS (70 eV) m/z (%): 292/294 (M/M+2,
72/5); 277 (29); 209 (100); 195 (22); 83 (4). HRMS: calc for C14H20N4OS 292.1358; found
292.1351.
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6-Cyclohexyl-3,7-dimethyl-2-(methylthio)-5,6-dihydropyrimido[4,5-d]pyrimidin-4(3H)-one
(3i) from 2f and trimethyl orthoacetate: yellow solid (53 %). Mp 235-40 ºC. IR (KBr): 3180
(b,w); 3124 (b,w); 2935 (b,w); 2886 (w); 1691 (m); 1641 (b,s); 1591 (s); 1523 (s); 1485 (m);
1
1405 (m). H-NMR (CDCl3) δ (ppm): 1.12 (tq, 3.7 Hz, 13.2 Hz, 1H); 1.27-1.40 (m, 2H); 1.69-
1.72 (m, 4H); 1.90 (pd, 13.8 Hz, 2H); 2.24 (s, 3H); 2.61 (s, 3H); 3.47 (s, 3H); 3.59-3.68 (m, 1H);
13
4.35 (s, 2H). C-NMR (CDCl3) δ (ppm): 15.0 p; 22.8 p; 25.1 s; 25.6 s; 29.1 s; 29.9 p; 39.4 s;
59.0 t; 92.9 q; 158.0 q; 160.9 q; 161.8 q; 164.0 q. MS (70 eV) m/z (%): 305/307 (M/M+2, 26/7);
223 (100); 209 (17); 177 (10); 83 (20). HRMS: calc for C15H22N4OS 306.1514; found 306.1509.
6-Benzyl-3-methyl-5,6-dihydropyrimido[4,5-d]pyrimidin-2,4(1H,3H)-dione (3j) from 2b,
triethyl orthoformate and 0.06 ml of acetic acid for 5 minutes: yellow solid (25%). Mp 239-41
ºC. IR (KBr): 3097 (b,w); 2883 (b,w); 2782 (b,w); 1709 (m); 1662 (s); 1625 (s); 1581 (m); 1453
1
(b,m); 1436 (m). H-NMR (DMSO-d6) δ (ppm): 3.03 (s, 3H); 3.94 (s, 3H); 4.48 (s, 2H); 7.35-
7.43 (m, 5H); 7.67 (s, 1H); 10.90 (ws, 1H). 13C-NMR (DMSO-d6) δ (ppm): 26.0 p; 41.5 s; 55.8 s;
82.0 q; 128.0 t; 128.1 t; 128.6 t; 134.3 q; 150.2 q; 150.7 q; 156.6 t; 161.5 q. MS (70 eV) m/z (%):
270 (M+, 4); 179 (29); 91 (100); 65 (25). HRMS: calc for C14H14N4O2 270.1117; found
270.1116.
Synthesis of pyrimido[4,5-d]pyrimidines (4) by reaction with carbonyl compounds: general
procedure. The 6-amino-5-(aminomethyl)pyrimidine (2) (1 mmol) in a solvent (3ml), the
carbonyl compound (1 mmol) and catalytic acid (0.05 mmol) were stirred and heated to 50 ºC.
for the indicated time. The solution was then cooled to room temperature, The product was
collected by filtration, washed with cold diethyl ether and recrystallized from EtOH.
6-Benzyl-3,7,7-trimethyl-2-methoxy-5,6,7,8-tetrahydropyrimido[4,5-d]pyrimidin-4(3H)-one
(4a) from 2b in EtOH, acetone and p-TsOH·H2O. Reaction time: 20h. Colorless solid (70%).
Mp 222 ºC. IR (KBr): 3285 (s); 2962 (m); 2801 (w); 2769 (w); 1639 (s); 1616 (s); 1598 (s); 1531
(s); 1223 (s). 1H-NMR (CDCl3). δ (ppm): 1.45 (s, 6H); 3.32 (s, 3H); 3.60 (s, 2H); 3.61 (s, 2H);
3.93 (s, 3H); 4.83 (s, 1H); 7.20 (pt, 7.0 Hz, 1H); 7.25-7.35 (m, 4H). 13C-NMR (CDCl3). δ (ppm):
27.00 p; 27.14 p; 43.38 s; 53.19 s; 55.10 p; 69.45 q; 85.70 q; 126.74 t; 128.26 t; 128.39 t; 140.06
q; 154.64 q; 155.86 q; 161.48 q. MS (70eV) m/z (%): 314 (M+, 9); 299 (46); 223 (16); 207 (35);
194 (18); 168 (95); 146 (45); 91 (100). HRMS: calc for C17H22N4O2 314.1743; found 314.1730.
6-Benzyl-3,7,7-trimethyl-2-(methylthio)-5,6,7,8-tetrahydropyrimido[4,5-d]pyrimidin-4(3H)-
one (4b) from 2e in EtOH, acetone and p-TsOH·H2O. Reaction time: 22h. Colorless solid (74%).
Mp 219-21 ºC. IR (KBr): 3293 (s); 2993 (w); 2927 (w); 2840 (w); 1628 (s); 1595 (s); 1539 (s);
1497 (s); 1164 (m). 1H-NMR (CDCl3). δ (ppm): 1.46 (s, 6H); 2.51 (s, 3H); 3.43 (s, 3H); 3.60 (s,
2H); 3.63 (s, 2H); 4.89 (s, 1H); 7.20 (pt, 7.0 Hz, 1H); 7.25-7.35 (m, 4H).13C-NMR (CDCl3).
δppm: 14.66 p; 27.07 p; 29.55 p; 43.25 s; 53.20 s; 69.39 q; 87.78 q; 126.79 t; 128.29 t; 128.38 t;
139.95 q; 154.52 q; 160.84 q. MS (70eV) m/z (%): 330 (M , 7); 315 (49); 223 (33); 210 (17);
+
184 (55); 146 (65); 91 (100). HRMS: calc for C17H22N4OS 330.1514; found 330.1511.
6-Benzyl-2-methoxy-3-methyl-7-phenyl-5,6,7,8-tetrahydropyrimido[4,5-d]pyrimidin-4(3H)-
one (4c) from 2b in EtOH, benzaldehyde and p-TsOH·H2O. Reaction time: 1h 30min. 10 ml of
water is added to the reaction mixture and neutralized with NaHCO3, extracted with DCM (20ml
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× 3) and dried with Na2SO4. The solvent is evaporated under reduced pressure. Colorless solid
(72%). Mp 168-70 ºC. IR (KBr): 3301 (m, b); 3026 (w); 2942 (w); 2903 (w); 2850 (w); 1658 (s,
b); 1608 (m); 1548 (s); 1519 (s, b); 1428 (m). 1H-NMR (CDCl3). δ (ppm): 3.33 (s, 3H); 3.47 (d,
15.9Hz, 1H); 3.58 (d, 15.9Hz, 1H); 3.67 (d, 13.2Hz, 1H); 3.73 (d, 13.2Hz, 1H); 3.99 (s, 3H);
13
5.07 (bs, 1H); 5.16 (bs, 1H); 7.26-7.44 (m, 10H). C-NMR (CDCl3). δ (ppm): 27.21 p; 43.00 s;
55.23 p; 56.97 s; 71.24 t; 86.18 q; 126.82 t; 127.22 t; 127.98 t; 128.38 t; 128.46 t; 128.97 t;
138.77 q; 141.04 q; 154.72 q; 155.94 q; 161.41 q. MS (70eV) m/z (%): 361 (M+-1, 50); 285 (59);
271 (59); 257 (45); 242 (41); 168 (83); 91(100). HR MS: calc for C21H22N4O2 362.1743; found
362.1732.
Crystal data for 4c were deposited at CCDC with reference CCDC 945842: Chemical formula
C21H22N4O2, Mr 362.43, Monoclinic, C2/c, 120 K, cell dimensions a, b, c (Å) 21.527 (3),
11.1709 (8), 17.448 (4); α, β, γ (°) 90, 120,144 (11), 90, V (Å3) 3628,5 (10), Z= 8, F(000)=1200,
Dx (Mg m-3) = 1.426, Mo Kα, ꢀ (mm-1)=0.10, Crystal size (mm)= 0.32 × 0.25 × 0.22. Data
collection: Diffractometer KappaCCD diffractometer, Monochromator graphite, CCD rotation
images, thick slices φ & θ scans, absorption correction SADABS 2.10, Tmin, Tmax 0.9724, 0.9809.
No. of measured, independent and observed [I > 2σ(I)] reflections 27121, 4163, 2179, Rint=
0.095, θ values (°): θmax = 27.5, θmin = 5.0; Range h = -23→23, k = -10→8, l = -22→24,
Refinement on F2:R[F2 > 2σ(F2)]=0.058, wR(F2)=0.167, S=1.07. No. of reflections 4163, No. of
2
parameters 246, No. of restraints 0. Weighting scheme: w = 1/[σ2(Fo ) + (0.0505P)2 + 1.7324P]
where P = (Fo + 2Fc2)/3. (ꢁ/σ)max< 0.001, ꢁσmax, ꢁσmin (e Å-3) 0.25, -0.31.
2
6-Benzyl-3-methyl-2-(methylthio)-7-phenyl-5,6,7,8-tetrahydropyrimido[4,5-d]pyrimidin-
4(3H)-one (4d) from 2e in EtOH, benzaldehyde and p-TsOH·H2O. Reaction temperature: reflux.
Reaction time: 40min. Colorless solid (55%). Mp 155-7 ºC. IR (KBr): 3261 (m, b); 3030 (w);
2842 (w); 1654 (s); 1629 (s); 1595 (s); 1527 (s); 1508 (s); 1073 (m). 1H-NMR (CDCl3). δ (ppm):
2.55 (s, 3H); 3.44 (s, 3H); 3.49 (d, 16.4Hz, 1H); 3.60 (d, 16.4Hz, 1H); 3.67 (d, 13.5Hz, 1H); 3.73
(d, 13.5Hz, 1H); 5.08 (s, 1H); 5.26 (s, 1H); 7.26-7.44 (m, 10H). 13C-NMR (CDCl3). δ (ppm):
14.72 p; 29.62 p; 42.81 s; 57.03 s; 71.08 t; 88.21 c; 126.79 t; 127.22 t; 128.00 t; 128.37 t; 128.46
t; 128.93 t; 138.66 q; 140.98 q; 154.54 q; 160.76 q; 160.88 q. MS (70eV) m/z (%): 378 (M+, 38);
301 (57); 287 (48); 273 (38); 256 (22); 184 (62); 91(100); 88 (34). HRMS: calc for C21H22N4OS
378.1514; found 378.1508.
6-Cyclohexyl-3-methyl-2-methoxy-5,6,7,8-tetrahydropyrimido[4,5-d]pyrimidin-4(3H)-one
(4e) from 2c in EtOH and p-TsOH·H2O. Reaction time: 15h. Colorless solid (40%). Mp 260-3
ºC. IR (KBr): 3251 (m, b); 2927 (m); 2853 (m); 1640 (s, b); 1607 (m); 1557 (s); 1527 (s); 1462
(m); 1415 (m). 1H-NMR (CDCl3). δ (ppm): 1.10-1.29 (m, 5H); 1.60 (pd, 11.2 Hz, 1H); 1.74-1.81
(m, 2H); 1.97 (pd, 10.3 Hz, 2H); 2.44-2.52 (m, 1H); 3.33 (s, 3H); 3.76 (s, 2H); 3.91 (s, 3H); 4.23
13
(d, 2.9Hz, 2H); 4.78 (bs, 1H). C-NMR (CDCl3). δ (ppm): 25.43 s; 25.94 s; 27.18 p; 30.63 s;
43.97 s; 55.12 p; 58.39 t; 59.60 s; 87.51 q; 155.68 q; 156.24 q; 161.27 q. MS (70eV) m/z (%):
278 (M+, 53); 277 (100); 195 (76); 180 (98); 168 (58); 72 (26); 55 (34). HRMS: calc for
C14H22N4O2 278.1743; found 278.1738.
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6-Cyclohexyl-3-methyl-2-(methylthio)-7-phenyl-5,6,7,8-tetrahydropyrimido[4,5-d]pyrimi-
din-4(3H)-one (4f) From 2f in EtOH, benzaldehyde and (±)camphor-10-sulfonic acid. Reaction
time: 22h. Colorless solid (67%). Mp 189-90 ºC. 1H-NMR (CDCl3). δ (ppm): 1.11-1.50 (m, 5H);
1.57 (bs, 1H); 1.69-1.83 (m, 2H); 1.89 (pd, 12.4 Hz, 1H); 1.98 (pd, 12.4 Hz, 1H); 2.49-2.58 (m,
4H); 3.32 (d, 16.7Hz, 1H); 3.43 (s, 3H); 3.80 (d, 16.7Hz, 1H); 5.22 (s, 1H); 5.41 (s, 1H); 7.22-
13
7.40 (m, 5H). C-NMR (CDCl3). δ (ppm): 14.7 p; 25.4 s; 25.5 s; 26.0 s; 29.6 p; 30.5 s; 31.9 s;
58.4 t; 69.8 t; 89.5 c; 126.8 t; 127.7 t; 128.4 t; 142.0 q;155.2 q; 160.2 q; 160.6 q. IR (KBR): 3332
(m, b); 2930 (m); 2851 (m); 1644 (s, b); 1593 (s); 1581 (s); 1511 (s, b); 1073 (m). MS (70eV)
m/z (%): 370 (M+, 64); 369 (42); 355 (32); 293 (83); 287 (82); 272 (100); 184 (56); 98 (30); 88
(60). HRMS: calc for C20H26N4OS 370.1827; found 370.1823.
3-Methyl-2-(methylthio)-7(R)-phenyl-6-[(R)-1-phenylethyl]-5,6,7,8-tetrahydropyrimido-
[4,5-d]pyrimidin-4(3H)-one (4g1) from 2g in CH3CN, benzaldehyde and (R)-camphor-10-
sulfonic acid (CSA-R). Reaction time: 18h. Colorless solid (66%). Mp 160-2 ºC. [α]D +84.4
(DCM; 25ºC; 0.01g/l). 1H-NMR (CDCl3). δ (ppm): 1.39 (d, 6.6Hz, 3H); 2.56 (s, 3H); 3.31 (d,
17.2Hz, 1H); 3.45 (s, 3H); 3.73 (q, 6.6Hz, 1H); 4.07 (dd, 1.9 y 17.2Hz, 1H); 4.98 (d, 3.5Hz, 1H);
5.14 (d, 3.5Hz, 1H); 7.23-7.29 (m, 6H); 7.34-7.36 (m, 2H); 7.50-7.55 (m, 2H). 13C-NMR
(CDCl3). δ (ppm): 14.7 p; 21.8 p; 36.9 s; 58.7 t; 69.8 t; 87.2 c; 126.5 t; 127.6 t; 128.3 t; 128.6 t;
129.0 t; 129.7 t; 134.4 t; 142.1 q; 145.4 q; 154.9 q; 160.6 q; 160.9 q. IR (KBR): 3266 (m, b);
3030 (w); 2975 (w); 2928 (w); 2865 (w); 1700 (m); 1638 (s); 1595 (s); 1539 (s); 1510 (s); 1554
(m); 1413 (m). MS (70eV) m/z (%): 392 (M+, 14); 315 (15); 287 (100); 273 (22); 258 (30); 184
(43); 105 (71); 88 (22). HRMS: calc for C22H24N4OS 392.1671; found 392.1667.
3-Methyl-2-(methylthio)-7(S)-phenyl-6-[(S)-1-phenylethyl]-5,6,7,8-tetrahydropyrimido-
[4,5-d]pyrimidin-4(3H)-one (4g4) from 2g′ in CH3CN, benzaldehyde and (S)-camphor-10-
sulfonic acid (CSA-S). Reaction time: 15h. Colorless solid (68%). [α]D -77.2 (DCM; 25ºC;
0,01g/l). 1H-NMR (CDCl3). δ (ppm): 1.39 (d, 6.6Hz, 3H); 2.56 (s, 3H); 3.31 (d, 17.2Hz, 1H);
3.45 (s, 3H); 3.73 (q, 6.6Hz, 1H); 4.07 (dd, 1.9 y 17.2Hz, 1H); 4.98 (d, 3.5Hz, 1H); 5.14 (d,
3.5Hz, 1H); 7.23-7.29 (m, 6H); 7.34-7.36 (m, 2H); 7.50-7.55 (m, 2H). 13C-NMR (CDCl3). δ
(ppm): 14.7 p; 21.8 p; 36.9 s; 58.7 t; 69.8 t; 87.2 c; 126.5 t; 127.6 t; 128.3 t; 128.6 t; 129.0 t;
129.7 t; 134.4 t; 142.1 q; 145.4 q; 154.9 q; 160.6 q; 160.9 q.
3-Methyl-2-(methylthio)-7(S)-phenyl-6-((R)-1-phenylethyl)-5,6,7,8-tetrahydropyrimido[4,5-
d]pyrimidin-4(3H)-one (4g2); 3-methyl-2-(methylthio)-7(R)-phenyl-6-[(S)-1-phenylethyl]-
5,6,7,8-tetrahydropyrimido[4,5-d]pyrimidin-4(3H)-one (4g3) 1H-NMR (CDCl3). δ (ppm): 1.49
(d, 6.6 Hz, 3H); 2.55 (s, 3H); 3.18 (d, 17.2 Hz, 2H); 3.39 (s, 3H); 3.80 (q, 6.6 Hz, 1H); 5.30 (d,
13
3.5Hz, 1H); 5.52 (bs, 1H); 7.19-7.53 (m, 5H). C-NMR (CDCl3). δ (ppm): 14.7 p; 21.9 p; 29.5
p; 39.5 s; 58.9 t; 68.4 t; 88.8 q; 126.7 t; 127.0 t; 127.3 t; 127.5 t; 127.7 t; 128.5 t; 141.6 c; 144.9
q; 155.0 q; 160.4 q; 160.7 q.
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Methods of calculations
Multidimensional conformational analysis (MDCA). From the concepts of MDCA32 we
performed a systematic conformational search for compounds 4g1-4. In such analysis the
following variables were taken into account:
(i) The three torsional angles φ1, φ2 and φ3, which determine the different conformations.
(MDCA predicts a multiplicity of 3 for the torsional angle φ1 and a multiplicity of 2 for the
torsional angles φ2 and φ3).
(ii) The two possible spatial orderings for the N atom of ring B (up or down)(multiplicity 2)
(iii) The two possible spatial orderings, axial or equatorial, for the alkyl-phenyl substituent (ring
D) (multiplicity 2).
(iv) The different configurational isomers due to both chiral centers (see figure 4) (multiplicity 2
for each chiral center).
Considering the above variables the conformational potential energy hypersurface (CPEH) might
be raised as follow:
E=E(φ1,φ2,φ3,up/down,ax/eq,R/S,R/S)
Equation 1 might be also expressed in function of the multiplicities as follows:
E=E(3x2x2x2x2x2)=192 eq. 2
eq. 1
Equation 2 indicates that in theory there are 192 different forms for compounds 4g1-4. However,
our preliminary calculations indicate that the torsional angles φ2 and φ3 adopt only two almost
perpendicular conformations. Considering that rings C and D are symmetrical, they give non-
identical but indistinguishable forms (energetically degenerate). Thus, Equation 2 might be
reduced to Equation 3.
E=E(3x2x2x2x2)=48
eq. 3
On the basis of Equation 3 MDCA predicts 48 different forms. All these different spatial
orderings were analyzed in our study.
Computations. An extensive search for the low energy conformations on the PEHS was carried
out by using a systematic search in connection with semiempirical PM6 calculations. Next to
determine the minima on the PEHS, fully relaxed DFT optimizations were performed.
Correlation effects were included using density functional theory (DFT) with the Beke-Lee-Yang
Parr (B3LYP)39-41 functional and the 6-31 G(d) basis set. Minima were characterized through
harmonic frequency analysis employing B3LYP/6-31 G(d) calculations. GIAO33-34 (gauge
independent atomic orbital) computations were carried out using B3LYP/6-31G(d) calculations.
All the calculations reported here were performed using the Gaussian 03 Program.35
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From the 48 potentially available conformations of compound 4g, only 41 conformers were
obtained for these molecules; seven conformations were annihilated during the optimization
process. Annihilation means that they do not converge or finally converge to one of the other 41
conformers. It should be noted that the synthesis of compound 4g1-4 was carried out from a
particular enantiomer in the first chiral center C(1′), so that the result of the synthesis can only
give rise to two stereoisomers R/R and R/S or S/S and S/R (C(1′)/C(7)). This assumption was
supported by the theoretical calculations performed here.
Considering an energetic window of 6 Kcal/mol just eight conformers were obtained for both
diasteromers (R/R and R/S) and their equivalents (S/S and S/R) (see Table 1S and Figure 4S in
supporting information for angles analyzed in this study). All these conformations were
optimized at DFT level using B3LYP/6/31G(d) calculations. These conformers and their relative
energies are summarized in Table 1S. Figure 3S shows a spatial view of the lowest-energy
conformation obtained for compound 4g2.
From the low-energy conformations obtained for both diasteromers R/R and R/S we calculated
the shielding tensors using the GIAO approach33,34 from the program Gaussian 03.35 From the
tensors we obtain the value of calculated chemical shift (δcalc) for each C atom of each isomer,
using the following expression (Eq. 4):
δcalc = b + m.(I + A)
eq. 4
where b and m values were obtained from the linear correlation between δexp and the sum of I
(isotropy) with A (asymmetry). Recently we demonstrated the importance to include asymmetry
in such calculations for this type of molecule.42-43
Acknowledgements
The authors thank “Centro de Instrumentación Científico-Técnica of Universidad de Jaén” and
the staff for data collection, and Universidad de Jaén (project reference UJA_07_16_33), the
Consejería de Innovación, Ciencia y Empresa (Junta de Andalucía, Spain) and Ministerio de
Ciencia e Innovación (Project reference SAF2008-04685-C02-02) for financial support. This
paper was partially supported by ANPCyT and UNSL-Argentina. R.D.E. is a member of the
CONICET (Argentina) staff.
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