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Article

Synthesis and Potent Antimicrobial Activity of Some Novel N-(Alkyl)-2-Phenyl-1H-Benzimidazole-5-Carboxamidines

by
Hakan Göker
1,*,
Mehmet Alp
1 and
Sulhiye Yıldız
2
1
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100 Tandogan, Ankara-Turkey
2
Department of Microbiology, Faculty of Pharmacy, Ankara University, 06100 Tandogan, Ankara, Turkey
*
Author to whom correspondence should be addressed.
Molecules 2005, 10(11), 1377-1386; https://doi.org/10.3390/10111377
Submission received: 7 June 2005 / Revised: 25 October 2005 / Accepted: 26 November 2005 / Published: 30 November 2005

Abstract

:
A series of 22 novel 1,2-disubstituted-1H-benzimidazole-N-alkylated-5-carboxamidine derivatives were synthesized and evaluated for in vitro antibacterial activity against S. aureus and methicillin resistant S. aureus (MRSA), E. coli, E. faecalis and for antifungal activity against C. albicans. Compound 59 [1-(2,4-dichlorobenzyl)-N-(2-diethylaminoethyl)-1H-benzimidazole-5-carboxamidine], with a 3,4-dichlorophenyl group at the C-2 position, displayed the greatest activity (MIC = 3.12 μg/mL against both some bacteria and the fungus C. albicans).

Introduction

We have already reported the synthesis of a series of 1,2-disubstituted-1H-benzimidazole-N-alkylated-5-carboxamidine derivatives and their very potent antibacterial activities against S. aureus and methicillin resistant S. aureus [1]. The study revealed that compounds I–IV (Figure 1) exhibited the best activity, with MIC values of 0.78 - 0.39 μg/mL against these species. As part of a continuing program focused on development of new antimicrobial benzimidazole carboxamidines, we planned to modify the structure of compounds I–IV.
Figure 1.
Figure 1.
Molecules 10 01377 g001

Results and Discussion

Chemistry

Syntheses of the target benzimidazoles (Table 1, Table 2) were achieved by two different methods, as shown in Scheme 1.
Scheme 1.
Scheme 1.
Molecules 10 01377 g002
Method A involved nucleophilic displacement in DMF of the chloro group of 4-chloro-3-nitro-benzonitrile by reaction with several amines to give 1–8 (Table 3). The cyano group was then converted into the imidate ester, using a modified Pinner method [1], and the imidate esters were used directly to make the corresponding benzamidines 9–18 (Table 4). Their reduction with H2, Pd/C produced 19–28 (Table 5). Condensation of these derivatives with the Na2S2O5 adducts of several benzaldehydes afforded the corresponding benzimidazoles 45–52, 55 and 59–61 [2]. Method B involved cyclization of 29–32 with the Na2S2O5 adducts of various benzaldehydes to afford 5-cyano-benzimidazoles 33–39 (Table 6), following this, the cyano groups were converted into the imidate esters, as in method A, and these were used to prepared the corresponding amidine compounds 40–44, 53, 54 and 56–58. For its practical advantages this method was used in particular for cyano-benzimidazoles, which have better solubility in EtOH, although the yields were low.
Table 1. Formulas and in vitro antibacterial and antifungal activities of 40 - 61. Molecules 10 01377 i001
Table 1. Formulas and in vitro antibacterial and antifungal activities of 40 - 61. Molecules 10 01377 i001
No.SubstituentsMinimal inhibitory concentration, μg/mL
R’R1R2R3R4S .a.MRSAMRSA*E. c.E. f.C. a.
40 Cl >50>50>50>50>50>50
41CH(CH3)2 Cl Cl>50>50>50>50>50>50
42CH(CH3)2 F>50>50>50>50>50>50
43 (Et)2NCH2CH2 F>50>50>50>50>50>50
44(Me)2NCH2CH2 Cl >50>50>50>50>50>50
45(Me)2NCH2CH2 ClCl12.512.512.5>505012.5
46CH(CH3)2CH3 CN>50>50>50>50>50>50
47CH(CH3)2CH3 OCH3OCH3>50>50>50>50>50>50
48Cyclopropyl COOCH3>50>50>50>50>50>50
49PhCH2 COOH>50>50>50>50>50>50
50PhCH2 COOCH312.5253.12>505025
51Cyclohexyl COOH>50>50>50>50>50>50
52 n-butyl >50>50>50>50>50>50
53(Me)2NCH2CH2n-butyl F>50>50>50>50>50>50
54CH(CH3)2CH(CH3)2 F>50>50>50>50>50>50
55(Me)2NCH2CH2Ph ClCl12.53.1212.5>502512.5
56(Me)2NCH2CH2PhCH2 ClCl12.512.512.5>502512.5
57(Et)2NCH2CH2PhCH2 ClCl12.512.56.255012.512.5
58(Me)2NCH2CH2PhCH2Cl Cl5012.512.5>505025
59(Et)2NCH2CH22,4-di-Cl- benzyl ClCl3.123.123.1212.56.253.12
60(Et)2NCH2CH2PhCH2CH2 OCH3OCH3>50>50>50>50>50>50
61IsobutylPhCH2CH2 ClCl6.256.256.25>5012.512.5
Ref OH t-butyl0.780.780.78
Sult 0.392525 1.56
Amp 0.78 50 0.78
Cip 0.39
Flu 1.56
S.a.: Staphylococcus aureus (ATCC 25923); MRSA (methicillin resistant Staphylococcus aureus, ATCC 43300); MRSA* (Methicillin resistant Staphylococcus aureus, clinical isolate); E. c.: Escherichia coli (ATCC 25922); E. f.: E. faecalis (ATCC 29212); C. a.: Candida albicans (ATCC 10231); Ref: this compound was found to be the most active compound against S. aureus by Weidner-Wells et al [3]; Sult: Sultamicillin; Amp: Ampicillin; Cip: Ciprofloxacin; Flu: Fluconazole

Antimicrobial Activity

The benzimidazoles 40–61 were tested by the macro-broth dilution [4] assay for in vitro antibacterial activity against Gram positive Staphylococcus aureus, methicillin resistant Staphylococcus aureus (MRSA, a clinical isolate from a wound), Enterococcus faecalis and Gram negative Escherichia coli and for antifungal activity against Candida albicans. The MIC values are listed in Table 1. The synthesized compounds and reference drugs were dissolved in water or DMSO-water (40 %) at a concentration of 400 μg/mL. The concentration was adjusted to 100 μg/mL by four- fold dilution with media culture and bacteria solution at the first tube. Data was not taken for the initial solution because of the high DMSO concentration (10 %). We have already reported that 3,4-dichloro substitution on the 2-phenyl group of amidinobenzimidazoles plays an important role in their antibacterial activity [1]. Thus, the most active compound, 59, and less active compounds 45, and 5557 all have a 3,4-dichlorophenyl group at the C-2 position. Replacement of 3,4-dichloro substitution with other functions such as fluoro, cyano, methoxy, carboxyl or methyl ester caused a reduction in inhibitory activities, and only compound 50, having a methyl ester group, exhibited moderate activity against MRSA with a MIC of 3.12 μg/mL. More lipophilic substituents on the benzimidazole N-atom such as phenyl, benzyl and 2,4-dichlorobenzyl do lead to quite active compounds (55–59), however substitution with methyl, butyl and isopropyl (cf. 46, 47, 52–54) gave no significant activity. Introduction of N,N-diethylaminoethyl substitution on the cationic amidine 59 led to inhibitory activity against E. coli and C. albicans. This is a very important result, as it represents the first example to date of inhibitory activity against E. coli with these amidinobenzimidazoles. Except for compound 59, none of the compounds showed important inhibitory activity against E. faecalis and C. albicans.

Conclusions

Introduction of aromatic amidine groups into the benzimidazole system gives a good profile of Gram-positive antibacterial activity. In particular, 1-(2,4-dichlorobenzyl)-N-(2-diethylaminoethyl)-1H-benzimidazole-5-carboxamidine (59), having a 3,4-dichlorophenyl at the C-2 position, exhibited the greatest activity, with a MIC value of 3.12 μg/mL against S. aureus and MRSA. Detailed mechanistic studies are required to understand the potent activity of this compound.

Experimental

General

Uncorrected melting points were measured on an Electrothermal 9100 capillary melting point apparatus. 1H-NMR spectra were recorded employing a Varian Mercury 400 MHz FT spectrometer, chemical shifts (δ) are in ppm relative to TMS, and coupling constants (J) are reported in Hertz. Mass spectra were taken on a Waters Micromass ZQ using the ESI(+) method. Microanalyses were performed by Leco CHNS-932. Some HCl salts of compounds 40–61 were prepared by using dry HCl gas in EtOH or isopropanol. All chemicals and solvents were purchased from Aldrich Chemical Co. or Fischer Scientific. Compounds 29–32 were synthesized as described in our previous study [2]
Table 2. Physical and spectral data for compounds 40 – 61.
Table 2. Physical and spectral data for compounds 40 – 61.

No

Mp
(OC)

Yield
(%)
Formula
Calculated
Found
1H-NMR
δ ppm (DMSO-d6)
(if not stated otherwise)

MS
(ESI+) m/z
Synthesis Method and Isolation
Column Chromatography
if not stated otherwise
40>30035C14H11ClN4 . 2HCl . H2O
C: 46.50 H: 4.18 N: 15.5
C: 46.24 H: 3.99 N: 15.3
7.59 - 7.97 (arom. 7H), 8.31 (s), 9.30 (s), 9.53 (s)271 (100)
273 (33)
(B)
Crys. Ethanolic HCl
41>29040C17H16Cl2N4. 2HCl . 1.5H2O
C: 45.66 H: 4.73 N: 12.5
C: 45.67 H: 4.45 N: 12.4
1.21 (d, 6H), 4.03 (m, 1H), 7.6 (m, 2H), 7.8(d, J=8.5, 1H), 7.83 (d, J=2, 1H), 7.92 (d, J=8.4, 1H), 8.05 (d, J=1.5, 1H), 9.06 (s), 9.42 (s), 9.54 (d)347 (100)
349 (65)
351 (11)
(B)
CH2Cl2 : Isopropanol : NH3 (100 : 60 : 4)
42>30028C17H17FN4. 2HCl . 1.5H2O
C: 51.52 H: 5.59 N: 14.1
C: 51.90 H: 5.31 N: 14.1
1.29 (d, 6H), 4.08 (m, 1H), 7.51 (t, 2H), 7.67 (d, J=8.3, 1H), 7.87 (d, J=8.4, 1H), 8.08 (s, 1H), 8.44 (m, 2H), 9.08 (s), 9.48 (s), 9.62 (d)297 (100)(B)
CH2Cl2 : Isopropanol : NH3 (100 : 60 : 3)
43>30041C20H24FN5. 3HCl . 2H2O
C: 48.15 H: 6.26 N: 14.1
C: 48.01 H: 6.02 N: 13.99
1.29 (t, 6H), 3.26 (4H), 3.46 (2H), 4.00 (2H), 7.56 (t, 2H), 7.84 (d, J=8.4, 1H), 7.92 (d, J=8.4, 1H), 8.28 (s, 1H), 8.52 (m, 2H), 9.67 (s), 9.93 (s), 10.21 (1H), 10.96 (s)354 (100)(B)
CH2Cl2 : Isopropanol : NH3 (100 : 60 : 3)
44100-110
bubb

37
* C18H20ClN5 . 4HCl . 1.5H2O.
0.5C2H6O
C: 42.27 H: 5.97 N: 12.97
C: 42.54 H: 6.04 N: 13.01
(CD3OD): 3.05 (6H), 3.66 (t, 2H), 4.03 (t, 2H), 7.69 (m, 1H), 7.82 (m, 2H), 7.99 (d, 1H), 8.102 (s, 2H), 8.54 (s, 1H)342 (100)
344 (33)
(B)
CH2Cl2 : Isopropanol : NH3 (100 : 60 : 3)
4595-100
bubb
18C18H19Cl2N5. 1.5HCl 0.25H2O . 0.25C3H8O
C: 49.99 H: 5.14 N: 15.54
C: 49.97 H: 5.14 N: 15.23
2.23 (s, 6H), 2.58 (t, 2H), 3.53 (t, 2H), 7.56 (dd, J=8.4, 1.6, 1H), 7.80 (d, J=8.8, 1H), 7.86 (d, J=8.4, 1H), 8.06 (s, 1H), 8.25 (dd, J= 8.4 1.8, 1H), 8.50 (d, J=1.8, 1H)376 (100)
378 (69)
380 (11)
(A)
CH2Cl2 : Isopropanol : Ethylamine (100 : 50 : 3)
46200-210
bubb
30C19H19N5 . 1.5H2O . 0.1C3H8O
C: 66.15 H: 6.55 N: 19.98
C: 66.19 H: 5.97 N: 19.82
1.23 (d, 6H), 3.95 (m, 1H), 3.97 (s, 3H), 7.76 (m, 2H), 8.09 (m, 5H)318 (100)(A)
CH2Cl2 : Isopropanol : Propylamine(100 : 50 : 4)
47100-110
bubb
26C20H24N4O2 . 1.8H2O
C: 62.42 H: 7.22 N: 14.55
C: 62.62 H: 6.94 N: 14.21
(DMSO-d6 + 1 drop D2O): 1.17 (d, 6H), 3.85-3.90 (10H), 7.15 (d, J=8.4, 1H), 7.4 (s, 2H), 7.62 (m, 2H), 7.97 (s, 1H)353 (100)(A)
CH2Cl2 : Isopropanol : Propylamine (100 : 50 : 3)
48285-290
bubb
60C19H18N4O2 . 3H2O . 0.3C3H8O
C: 58.80 H: 6.54 N: 13.78
C: 58.72 H: 6.20 N: 13.36
0.77 (2H), 0.91 (d, 2H), 2.79 (1H), 3.89 (s, 3H), 7.53 (d, J=8, 1H), 7.67 (d, J=8.4, 1H), 8.04 (s, 1H), 8.09 (d, J=7.8, 2H), 8.38 (d, J=8, 2H)335 (100)(A)
Cryst. Isopropanol
49260-270
bubb
34C22H18N4O2 . 2H2O
C: 65.01 H: 5.45 N: 13.77
C: 64.95 H: 5.23 N: 13.78

4.73 (s, 2H), 7.35-8.30 (aromat. 12H)
371 (100)(A)
Cryst. EtOH
50265-275
bubb
52C23H20N4O2 . 0.25H2O
C: 71.03 H: 5.31 N: 14.40
C: 71.07 H: 5.14 N: 14.32
3.88 (s, 3H), 4.53 (s, 2H), 7.27-7.56 (m, 7H), 8.03-8.06 (m, 3H), 8.37 (d, J=8.4, 2H),385 (100)(A)
CH2Cl2 : Isopropanol : Propylamine
(100 : 100 : 6)
51>30064C21H22N4O2 . 2HCl . 1.5H2O
C: 54.55 H: 5.88 N: 12.12
C: 54.26 H: 5.89 N: 12.62
1.21-1.42-1.63-1.77-1.98 (m, 10H), 3.78 (1H), 7.65 (d, J=8.4, 1H), 7.87 (d, J=8.4, 1H), 8.1 (s, 1H), 8.15 (d, J=8, 2H), 8.47 (d, J=7.6, 2H), 9.19 (s), 9.50 (s), 9.63 (d)363 (100)(A)
Cryst. Ethanolic HCl
52150-155
bubb
22C18H20N4. 2HCl . 2.2H2O 0.5C3H8O
C: 53.84 H: 7.04 N: 12.88
C: 53.98 H: *** N: 12.81
(Base) : 0.64 (t, 3H), 1.01 (m, 2H), 1.56 (m, 2H), 4.33 (t, 2H), 7.56 (m, 3H), 7.76 (m, 3H), 7.95 (d, J=8.6, 1H), 8.23 (d, J=1.4, 1H), 9.18 (s), 9.41 (s) 293 (100)(A)
CH2Cl2 : Isopropanol : NH3 (100 : 50 : 4)
53205-210 bubb32C22H28FN5 . 3HCl . 2H2O
C: 50.14 H: 6.69 N: 13.29
C: 50.34 H: 6.52 N: 12.92
0.78 (t, 3H), 1.20 (m, 2H), 1.70 (m, 2H), 2.90 (s, 6H), 3.51 (t, 2H), 4.03 (t, 2H), 4.45 (t, 2H), 7.55 (m, 2H), 8.01 (m, 3H), 8.10 (d, J=8.6, 1H), 8.42 (d, J=1.3, 1H), 9.77 (s), 9.97 (s), 10.28 (s)382 (100)(B)
CH2Cl2 : Isopropanol : Ethylamine (100 : 50 : 3)
54115-120
bubb
20C20H23FN4 . 3HCl . 1.25H2O
C: 51.07 H: 6.11 N: 11.91
C: 51.05 H: 6.31 N: 11.55
1.34 (d, 6H), 1.66 (d, 6H), 4.2 (m, 1H), 4.8 (m, 1H), 7.54 (m, 2H), 7.74 (d, J=8.7, 1H), 7.86 (m, 2H), 8.22 (2H), 9.21 (s), 9.58 (s), 9.68 (d)339 (100)(B)
CH2Cl2 : Isopropanol : Ethylamine (100 : 50 : 3)
55295-300
bubb
30C24H23Cl2N5 . 3HCl . 1.25H2O
C: 49.34 H: 4.91 N: 11.98
C: 49.45 H: *** N: 11.87
2.85 (s, 6H), 3.44 (t, 2H), 3.92 (t, 2H), 7.37-7.80 (m, 10H), 8.41 (d, J=1.2, 1H), 9.52 (s), 9.83 (s), 10.07 (s), 10.81 (s)452 (100)
454 (68)
456 (12)
(A)
CH2Cl2 : Isopropanol : NH3 (100 : 50 : 15)
56130-135
bubb
49C25H25Cl2N5 . 3HCl . 1.25H2O
C: 50.18 H: 5.14 N: 11.7
C: 50.06 H: 5.22 N: 11.49
2.90 (6H), 3.50 (t, 2H), 4.03 (q, 2H), 5.74 (s, 2H), 7.04 (m, 2H),7.34 (m, 3H), 7.82 (m, 4H), 8.02 (d, J=1.9, 1H), 8.42 (d, J=1.4, 1H), 9.71 (s), 9.86 (s), 10.15 (d), 11.14 (s)466 (100)
468 (68)
470 (11)
(B)
CH2Cl2 : Isopropanol : Ethylamine (100 : 50 : 5)
57120-130
bubb
46C27H29Cl2N5 . 3HCl . 2H2O
C: 50.68 H: 5.67 N: 10.94
C: 50.66 H: 5.62 N: 10.92
1.27 (t, 6H), 3.24 (4H), 3.45 (2H), 3.99 (2H), 5.72 (s, 2H), 6.98 (m, 2H), 7.27 (m, 3H), 7.81 (m, 4H), 8.01 (d, J=2, 1H), 8.35 (s, 1H), 9.61 (s), 9.81 (s), 10.11 (s), 10.97 (s)494 (100)
496 (68)
498 (12)
(B)
CH2Cl2 : Isopropanol : Ethylamine (100 : 50 : 3)
58**33** C25H25Cl2N5 . HCl(CD3OD): 3.29 (6H), 3.63 (t, 2H), 3.99 (t, 2H), 5.57 (s, 2H), 7.03 (m, 2H), 7.26 (m, 3H), 7.61 (dd, J=8.4 , 2, 1H), 7.68 (d, J=8.1, 1H), 7.82 (d, J=2, 1H), 7.95 (m, 2H), 8.42 (s, 1H)466 (100)
468 (71)
470 (13)
(B)
CH2Cl2 : Isopropanol : NH3 (100 : 50 : 0.5)
59120-125
bubb
35C27H27Cl4N5 . 3HCl . H2O
C: 46.64 H: 4.71 N: 10.07
C: 46.80 H: 4.82 N: 9.86
1.25 (t, 6H), 3.23 (m, 4H), 3.41 (t, 2H), 3.84 (2H), 5.71 (s, 2H), 6.73 (d, J=8.8, 1H), 7.30 (dd, J=8.4 2, 1H), 7.62-7.81 (m, 5H), 7.93 (d, J=2, 1H), 8.35 (s, 1H), 9.64 (s), 9.83 (s), 10.13 (s), 10.96 (s)562 (80)
564 (100)
566 (51)
568 (14)
(A)
CH2Cl2 : Isopropanol : NH3 (100 : 50 : 0.5)
60127-130
bubb.
30C30H37N5O2 . 3HCl . H2O
C: 54.34 H: 6.99 N: 10.56
C: 54.40 H: 6.80 N: 10.45
1.29 (t, 6H), 3.08 (t, 2H), 3.25 (4H), 3.48 (d, 2H), 3.84 (s,3H), 3.89 (s,3H), 4.04 (q, 2H), 4.83 (t, 2H), 6.9 (m, 2H), 7.12-7.31 (m, 6H), 8.03 (d, J=8.8, 1H), 8.27 (d, J=8.8, 1H), 8.36 (s, 1H), 9.87 (s), 10.08 (s), 10.44 (s), 11.1 (s)500 (100)(A)
CH2Cl2 : Isopropanol : iso-propylamine(90 : 30 : 2)
61288-29019C26H26Cl2N4 . 1.5HCl
C: 60.04 H: 5.33 N: 10.77
C: 60.05 H: 5.50 N: 10.66
0.96 (d,6H), 2.06 (m, 1H), 2.93 (t, 2H), 3.16 (t, 2H), 4.63 (t, 2H), 6.67 (d, J=7.2, 2H), 7.03 (t, J=7.2, 2H), 7.11 (m, 1H), 7.45 (2H), 7.70 (m, 2H), 8.01 (d, J=8.8, 1H), 8.12 (s, 1H), 9.02 (s), 9.44 (s), 9.75 (s)465 (100)
467 (67)
469 (11)
(A)
CH2Cl2 : Isopropanol : ethylamine(100 : 50 : 0.5)
* Hygroscopic; ** Very hygroscopic, not measurable; *** No satisfactory result.

4-(2,4-Dichlorobenzyl)amino-3-nitrobenzonitrile (7)

A mixture of 2,4-dichlorobenzylamine (3.52 g, 20 mmol) and 4-chloro-3-nitrobenzonitrile (2 g, 10.95 mmol) in DMF (3 mL) was heated under reflux for 4h at 120°C. The mixture was allowed to cool and EtOH was added. The resultant yellow precipitate was filtered, washed with water and crystallised from EtOAc-n-hexane; yield 57 %; mp: 192oC; 1H-NMR (CDCl3): 4.66 (d, J=5.6, 2H), 6.8 (d, J=9.2, 1H), 7.24 (m, 2H), 7.47 (d, J=2, 1H), 7.58 (dd, Jo=9.2, Jm=2, 1H), 8.55 (d, J=2, 1H), 8.78 (br.t, 1H).

4-(2-Phenylethyl)amino-3-nitrobenzonitrile (8)

2-Phenylethylamine (1.3 g, 10.8 mmol) and 4-chloro-3-nitrobenzonitrile (1g, 5.4 mmol) were allowed to react for 2 h, at 100oC and the product wasisolated as described for 7; yield 79 %; mp: 111oC; 1H-NMR (CDCl3): 3.04 (t, J=7.1, 2H), 3.61 (q, J=6.8, 2H), 6.89 (d, J=8.8, 1H), 7.25-7.37 (m, 4H), 7.58 (dd, Jo=8.8, Jm=2, 1H), 8.44 (br.t, 1H), 8.47 (d, J=2, 1H).
Table 3. Formulas and melting points of 1–8. Molecules 10 01377 i002
Table 3. Formulas and melting points of 1–8. Molecules 10 01377 i002
CompR1FormulaRef.
1HC7H5N3O2Commercial
2methylC8H7N3O2Lit [1]
3iso-propylC10H11N3O2Lit [2]
4n-butylC11H13N3O2Lit [2]
5phenylC13H9N3O2lit [5] 126oC, 126 oC
6benzylC14H11N3O2Lit [2]
72,4-dichlorobenzylC14H9Cl2N3O2---
8PhCH2CH2 C15H13N3O2---

General Procedure for Synthesis of 9–18, 40–44, 53, 54, 56–58

1–8 (4.5 mmol) and 33–39 (Table 6, 1 mmol) were suspended in absolute EtOH, cooled in a ice-salt bath, and dry HCl gas was passed through the solution for 40 min. The solution was stirred in a stoppered flask at room temperature for 3 days and then diluted with dry ether. The imidate esters precipitated as yellow solids, which were washed with ether then dried under vacuum at room temperature. All imidate esters were used directly without characterisation. A suspension of imidate ester HCl in absolute EtOH was stirred with corresponding the amines (1.5 - 2 fold excess) overnight at 25-30oC. The reaction mixture was evaporated and diluted with ether, the precipitate was filtered, washed with ether, then dried. Compounds 9–18 (Table 4) were used without purification as HCl salts for the next steps since they were prepared completely pure. In contrast, crude products 40–44, 53, 54, 56–58 were treated with dilute Na2CO3 solution, then water. Further purification methods are given in Table 2.
Table 4. Formulas, spectroscopic data, m.p. and yields of 9 - 18.
Table 4. Formulas, spectroscopic data, m.p. and yields of 9 - 18.
CompR’R1FormulaNMR
δ ppm (DMSO-d6)
Mass
(ESI+)
mp
(oC)
Yield (%)
9 butylC11H16N4O20.895 (t, 3H), 1.34 (m, 2H), 1.56 (m, 2H), 3.41 (q, 2H), 7.22 (d, J=9.2, 1H), 7.95 (dd, J=9.2, 2.4, 1H), 8.6 (t, 1H), 8.67 (d, J=2.4, 1H), 9.2 (br.s)237
(100)
200-462
10iso-propylmethylC11H16N4O2 Lit [1]
11(CH3)2N(CH2)2 C11H17N5O22.24 (s, 6H), 2.58 (t, 2H), 3.5 (t, 2H), 7.14 (d, J=8.8,1H), 7.5 (dd, J=8.8, 2, 1H), 8.09 (br.s, 2H), 8.48 (d, J=2, 1H).252
(100)
220-230
(bubb)
Lit [6]
12cyclo-propyl C10H12N4O2 Lit [1]
13cyclo-hexyl C13H18N4O2 Lit [1]
14Benzyl C14H14N4O2 Lit [1]
15(CH3)2N(CH2)2phenylC17H21N5O22.32 (s, 6H), 2.69 (2H), 3.4 (br.s), 3.56 (t, 2H), 7.12 (d, J=9..3, 1H), 7.28-7.49 (m, 5H), 7.85 (dd, J=9.2, 2.3, 1H), 8.61 (d, J=2.3, 1H), 9.85 (s, 1H)328
(100)
Hygros.
110
(bubb)
87
16iso-butylPhCH2CH2C19H24N4O2(CD3OD): 1.05 (d, 6H), 2.07 (m,1H), 3.05 (t, 2H), 3.25 (d, 2H), 3.72 (m, 2H), 7.21 (m, 2H), 7.3 (m, 4H), 7.79 (dd, J=9.2 2.4, 1H), 8.53 (t, 1H), 8.59 (d, J=2.4, 1H)341
(100)
247-975
17(C2H5)2N(CH2)2PhCH2CH2C21H29N5O2(CD3OD): 1.11 (t, 6H), 2.68 (q, 4H), 2.78 (t, 2H), 3.03 (t, 2H), 3.57 (t, 2H), 4.7 (s, 2H), 7.21 (m, 2H), 7.3 (m, 4H), 7.81 (dd, J=8.8 ,2.4, 1H), 8.62 (d, J=2.4, 1H).384
(100)
236-985
18(C2H5)2N(CH2)22,4-dichloro benzylC20H25Cl2N5O2(CD3OD): 1.11 (t, 6H), 2.68 (q, 4H), 2.79 (t, 2H), 3.57 (t, 2H), 4.78 (t, 2H), 6.98 (d, J=9.2, 1H), 7.30 (dd, J=8.6 2.4, 1H), 7.37 (d, J=8.8, 1H), 7.53 (d, J=2, 1H), 7.78 (dd, J=9.2, 2.4, 1H), 8.68 (d, J=2.4, 1H)438(100)
440 (65)
442 (12)
203-589
Table 5. Formulas, spectroscopic data, mp and yields of 19 - 28. Molecules 10 01377 i003
Table 5. Formulas, spectroscopic data, mp and yields of 19 - 28. Molecules 10 01377 i003
CompRR1FormulaNMR
δ ppm (DMSO-d6)
MS
(ESI+)
mp
(oC)
Yield
(%)
19 butylC11H18N40.88 (t, 3H), 1.36 (m, 2H), 1.56 (m, 2H), 3.1 (t, 2H), 5.01 (br.s, 2H), 5.57 (br.s, 2H), 6.46 (d, J=8, 1H), 6.9 (s, 1H), 7.07 (d, J=8.4, 1H), 8.58 (s, 2H), 8.74 (s, 2H).207(100)28594
20iso-propylmethylC11H18N4 Lit [1]
21(CH3)2N(CH2)2 C11H19N5(+ one drop D2O): 2.2 (s, 6H), 2.54 (t, 2H), 3.4 (t, 2H), 6.57 (d, J=8, 1H), 6.85 (m, 2H)222(100)Lit [6]
22cyclo-propyl C10H14N4 Lit [1]
23cyclo-hexyl C13H20N4 Lit [1]
24benzyl C14H16N4 Lit [1]
25(CH3)2N(CH2)2phenylC17H23N5(+ one drop D2O) : 2.27 (s, 6H), 2.63 (t, 2H), 3.5 (t, 2H), 6.85-7.26 (8H)298(100)*90
26iso-butyl-CH2CH2 PhC19H26N40.92 (d, 6H), 1.96 (m, 1H), 2.9 (t, 2H), 3.17 (t, 2H), 3.31(2H), 4.39 (t, 1H), 5.03 (2H), 5.66 (t,1H), 6.57 (d, J=8.4, 1H), 6.87 (d, J=1.6, 1H), 6.98 (dd, J=8.4 1.6, 1H), 7.2-7.3 (m, 5H), 8.57 (s, 1H), 8.9 (s, 1H)311(100)98-10094
27(C2H5)2N(CH2)2-CH2CH2 PhC21H31N5(CD3OD): 1.09 (t, 6H), 2.65 (q, 4H), 2.77 (t, 2H), 2.96 (t, 2H), 3.47 (t, 2H), 3.52 (t, 2H), 6.68 (d, J=8, 1H), 7.01 (d, J=2, 1H), 7.14-7.3 (m, 6H)354(100)*95
28(C2H5)2N(CH2)22,4-dichloro-benzylC20H27Cl2N5(CD3OD): 1.14 (t, 6H), 2.76 (4H), 2.89 (2H), 3.57 (t, 2H), 4.54 (s, 2H), 6.37 (d, J=8, 1H), 7.06 (d, J=2, 2H), 7.25 (dd, J=8.2 2, 1H), 7.31 (d, J=8.4, 1H), 7.49 (d, J=2, 1H)408(100)
410(65)
412(11)
*92
* No sharp melting point.

General Procedure for Synthesis of 1928

Compound 9–18 (3.5 mmol) in EtOH (75 mL) was subjected to hydrogenation using 40 psi of H2 and 10 % Pd-C (40mg) until uptake of H2 ceased. The catalyst was filtered on a bed of Celite, washed with EtOH, and the filtrate was concentrated in vacuo. The crude o-phenylenediamines (grey–purple– black in colour) were used for the subsequent steps without crystallisation (Table 5). In order to prevent halogen reduction of compound 28, 15 psi of H2 pressure was employed.
Table 6. Formulas, spectroscopic data, mp and yields of 33 - 39. Molecules 10 01377 i004
Table 6. Formulas, spectroscopic data, mp and yields of 33 - 39. Molecules 10 01377 i004
CompR1R2R3R4FormulaNMR
δ ppm (CDCl3)
Mass
(ESI+)
mp
(oC)
Yield
(%)
İsolation
33 Cl C14H8ClN3 Lit [2]
34 Cl ClC14H7Cl2N3 Lit [2]
35 FC14H8FN3 Lit [2]
36iso-propyl FC17H14FN3 Lit [2]
37n-butyl FC18H16FN3 Lit [2]
38benzyl ClClC21H13Cl2N35.47 (s, 2H), 7.05 (m, 2H), 7.3-7.55 (m,7H),7.82 (d, J=2, 1H), 8.16 (d, J=1.5, 1H)91(100)
378(50)
380(33)
382(6)
19275Cryst.
EtOH-water
39benzylCl ClC21H13Cl2N35.27 (s, 2H), 6.91(m, 2H), 7.26-7.57 (m, 8H), 8.16 (1H)91(100)
378(54)
380(31)
382(5)
195-673Cryst.
EtOH-water

General Procedure for Synthesis of 33–39, 45–52, 55, 59–61

The corresponding benzaldehydes (15 mmol) were dissolved in EtOH (50 mL) and sodium metabisulfite (1.6 g) in H2O (10 mL) was added in portions. The reaction mixture was stirred vigorously and more EtOH was added. The mixture was kept in a refrigerator for a several hours. The precipitate was filtered and dried (yields over 93 %). The mixture of these salts (1 mmol) and 19–28 and 29–32 (1 mmol) in DMF (1-2 mL) was heated at 120oC for 4h. The reaction mixture was cooled, poured into H2O, and the solid was filtered. Purification methods are given in Table 2 and Table 6.

Acknowledgments

This work was supported by Ankara University Research Fund (Project No: 0000018-2003). The Central Lab. of the Faculty of Pharmacy of Ankara University provided support for acquisition of the NMR, mass spectrometer and elemental analyser used in this work.

References

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  • Sample Availability : Available from the authors.

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MDPI and ACS Style

Göker, H.; Alp, M.; Yıldız, S. Synthesis and Potent Antimicrobial Activity of Some Novel N-(Alkyl)-2-Phenyl-1H-Benzimidazole-5-Carboxamidines. Molecules 2005, 10, 1377-1386. https://doi.org/10.3390/10111377

AMA Style

Göker H, Alp M, Yıldız S. Synthesis and Potent Antimicrobial Activity of Some Novel N-(Alkyl)-2-Phenyl-1H-Benzimidazole-5-Carboxamidines. Molecules. 2005; 10(11):1377-1386. https://doi.org/10.3390/10111377

Chicago/Turabian Style

Göker, Hakan, Mehmet Alp, and Sulhiye Yıldız. 2005. "Synthesis and Potent Antimicrobial Activity of Some Novel N-(Alkyl)-2-Phenyl-1H-Benzimidazole-5-Carboxamidines" Molecules 10, no. 11: 1377-1386. https://doi.org/10.3390/10111377

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