27318-90-7|1,10-Phenanthroline-5,6-dione| Ambeed

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Quality Control of [ 27318-90-7 ] Purity: 98% SDS Specification

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Crystal Structures of DNA Intercalating Agents Dipyrido[3,2-f:2′,3′-h]quinoxaline (dpq), (Benzo[i]dipyrido[3,2-a:2′,3′c]phenazine (dppn), and [Ir(ppy)2(dppn)][PF6] (Where Hppy = 2-Phenylpyridine)

Marisa James ; Madelyn R. Shevlin ; Thomas B. Green ; Megan M. Smart ; Colin D. McMillen ; Jared A. Pienkos

DOI: 10.3390/inorganics11090353 Inorganics,2023,11(9):353.

Abstract: Pyrazino-phenanthroline ligands are commonly used with transition metals as DNA intercalation agents. Herein, we report the characterization of two commonly utilized pyrazino-phenanthroline ligands, dipyrido[3,2-f:2′,3′-h]quinoxaline (dpq) and (benzo[i]dipyrido[3,2-a:2′,3′c]phenazine (dppn), by single-crystal X-ray diffraction. Additionally, the characterization of [Ir(ppy)2(dppn)][PF6], where Hppy = 2-phenylpyridine, by single-crystal X-ray diffraction is described. Both the dpq and dppn ligands crystallize as chloroform solvates where the chloroform molecule occupies the equivalent binding pocket of a metal in metal complexes of these ligands. These pyrazino-phenanthrolines are largely planar, with the dppn ligand displaying a slight twist. When the dppn ligand is coordinated to iridium(III), the dppn ligand on the resulting complex displays a significant degree of bending along the longitudinal direction of the ligand. This iridium (III) complex crystallizes as a CH2Cl2 and Et2O solvate and due to the volatility of these solvents these crystals are only stable for a few seconds outside of the mother liquor. The structures of the free ligands and the [Ir(ppy)2(dppn)][PF6] complex all display extensive π stacking interactions.

Keywords: pyrazino-phenanthroline ; dpq ; dppn ; intercalation ; iridium (III) complex

Purchased from AmBeed: 27318-90-7

Product Details of [ 27318-90-7 ]

CAS No. :	27318-90-7
Formula :	C₁₂H₆N₂O₂
M.W :	210.19
SMILES Code :	C1=C2C(=NC=C1)C3=C(C(=O)C2=O)C=CC=N3
MDL No. :	MFCD00014473
InChI Key :	KCALAFIVPCAXJI-UHFFFAOYSA-N
Pubchem ID :	72810

Safety of [ 27318-90-7 ]

GHS Pictogram:
Signal Word:	Warning
Hazard Statements:	H315-H319-H335
Precautionary Statements:	P261-P305+P351+P338

Computational Chemistry of [ 27318-90-7 ] Show Less

Physicochemical Properties

Num. heavy atoms	16
Num. arom. heavy atoms	12
Fraction Csp3	0.0
Num. rotatable bonds	0
Num. H-bond acceptors	4.0
Num. H-bond donors	0.0
Molar Refractivity	56.13
TPSA ? Topological Polar Surface Area: Calculated from Ertl P. et al. 2000 J. Med. Chem.	59.92 Å²

Lipophilicity

Log P_o/w (iLOGP)? iLOGP: in-house physics-based method implemented from Daina A et al. 2014 J. Chem. Inf. Model.	0.93
Log P_o/w (XLOGP3)? XLOGP3: Atomistic and knowledge-based method calculated by XLOGP program, version 3.2.2, courtesy of CCBG, Shanghai Institute of Organic Chemistry	0.55
Log P_o/w (WLOGP)? WLOGP: Atomistic method implemented from Wildman SA and Crippen GM. 1999 J. Chem. Inf. Model.	1.52
Log P_o/w (MLOGP)? MLOGP: Topological method implemented from Moriguchi I. et al. 1992 Chem. Pharm. Bull. Moriguchi I. et al. 1994 Chem. Pharm. Bull. Lipinski PA. et al. 2001 Adv. Drug. Deliv. Rev.	-0.4
Log P_o/w (SILICOS-IT)? SILICOS-IT: Hybrid fragmental/topological method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	2.46
Consensus Log P_o/w? Consensus Log P_o/w: Average of all five predictions	1.01

Water Solubility

Log S (ESOL):? ESOL: Topological method implemented from Delaney JS. 2004 J. Chem. Inf. Model.	-2.04
Solubility	1.9 mg/ml ; 0.00902 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Soluble
Log S (Ali)? Ali: Topological method implemented from Ali J. et al. 2012 J. Chem. Inf. Model.	-1.38
Solubility	8.76 mg/ml ; 0.0417 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Very soluble
Log S (SILICOS-IT)? SILICOS-IT: Fragmental method calculated by FILTER-IT program, version 1.0.2, courtesy of SILICOS-IT, http://www.silicos-it.com	-4.5
Solubility	0.00657 mg/ml ; 0.0000313 mol/l
Class? Solubility class: Log S scale Insoluble < -10 < Poorly < -6 < Moderately < -4 < Soluble < -2 Very < 0 < Highly	Moderately soluble

Pharmacokinetics

GI absorption? Gatrointestinal absorption: according to the white of the BOILED-Egg	High
BBB permeant? BBB permeation: according to the yolk of the BOILED-Egg	Yes
P-gp substrate? P-glycoprotein substrate: SVM model built on 1033 molecules (training set) and tested on 415 molecules (test set) 10-fold CV: ACC=0.72 / AUC=0.77 External: ACC=0.88 / AUC=0.94	No
CYP1A2 inhibitor? Cytochrome P450 1A2 inhibitor: SVM model built on 9145 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.83 / AUC=0.90 External: ACC=0.84 / AUC=0.91	Yes
CYP2C19 inhibitor? Cytochrome P450 2C19 inhibitor: SVM model built on 9272 molecules (training set) and tested on 3000 molecules (test set) 10-fold CV: ACC=0.80 / AUC=0.86 External: ACC=0.80 / AUC=0.87	No
CYP2C9 inhibitor? Cytochrome P450 2C9 inhibitor: SVM model built on 5940 molecules (training set) and tested on 2075 molecules (test set) 10-fold CV: ACC=0.78 / AUC=0.85 External: ACC=0.71 / AUC=0.81	No
CYP2D6 inhibitor? Cytochrome P450 2D6 inhibitor: SVM model built on 3664 molecules (training set) and tested on 1068 molecules (test set) 10-fold CV: ACC=0.79 / AUC=0.85 External: ACC=0.81 / AUC=0.87	No
CYP3A4 inhibitor? Cytochrome P450 3A4 inhibitor: SVM model built on 7518 molecules (training set) and tested on 2579 molecules (test set) 10-fold CV: ACC=0.77 / AUC=0.85 External: ACC=0.78 / AUC=0.86	Yes
Log Kp (skin permeation)? Skin permeation: QSPR model implemented from Potts RO and Guy RH. 1992 Pharm. Res.	-7.19 cm/s

Druglikeness

Lipinski? Lipinski (Pfizer) filter: implemented from Lipinski CA. et al. 2001 Adv. Drug Deliv. Rev. MW ≤ 500 MLOGP ≤ 4.15 N or O ≤ 10 NH or OH ≤ 5	0.0
Ghose? Ghose filter: implemented from Ghose AK. et al. 1999 J. Comb. Chem. 160 ≤ MW ≤ 480 -0.4 ≤ WLOGP ≤ 5.6 40 ≤ MR ≤ 130 20 ≤ atoms ≤ 70	None
Veber? Veber (GSK) filter: implemented from Veber DF. et al. 2002 J. Med. Chem. Rotatable bonds ≤ 10 TPSA ≤ 140	0.0
Egan? Egan (Pharmacia) filter: implemented from Egan WJ. et al. 2000 J. Med. Chem. WLOGP ≤ 5.88 TPSA ≤ 131.6	0.0
Muegge? Muegge (Bayer) filter: implemented from Muegge I. et al. 2001 J. Med. Chem. 200 ≤ MW ≤ 600 -2 ≤ XLOGP ≤ 5 TPSA ≤ 150 Num. rings ≤ 7 Num. carbon > 4 Num. heteroatoms > 1 Num. rotatable bonds ≤ 15 H-bond acc. ≤ 10 H-bond don. ≤ 5	0.0
Bioavailability Score? Abbott Bioavailability Score: Probability of F > 10% in rat implemented from Martin YC. 2005 J. Med. Chem.	0.55

Medicinal Chemistry

PAINS? Pan Assay Interference Structures: implemented from Baell JB. & Holloway GA. 2010 J. Med. Chem.	2.0 alert
Brenk? Structural Alert: implemented from Brenk R. et al. 2008 ChemMedChem	1.0 alert: heavy_metal
Leadlikeness? Leadlikeness: implemented from Teague SJ. 1999 Angew. Chem. Int. Ed. 250 ≤ MW ≤ 350 XLOGP ≤ 3.5 Num. rotatable bonds ≤ 7	No; 1 violation:MW<1.0
Synthetic accessibility? Synthetic accessibility score: from 1 (very easy) to 10 (very difficult) based on 1024 fragmental contributions (FP2) modulated by size and complexity penaties, trained on 12'782'590 molecules and tested on 40 external molecules (r² = 0.94)	2.38

Application In Synthesis of [ 27318-90-7 ]

* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.

Downstream synthetic route of [ 27318-90-7 ]

[ 27318-90-7 ] Synthesis Path-Downstream 1~26

1
[ 27318-90-7 ]
[ 4506-66-5 ]
5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)porphyrin-2,3-dione [ No CAS ]
C₉₄H₁₀₀N₁₀ [ No CAS ]

References: [1]Journal of the Chemical Society. Chemical communications,1995,p. 1921 - 1924.

2
[ 27318-90-7 ]
[ 4506-66-5 ]
C₈₂H₉₄N₈O₄ [ No CAS ]
C₁₀₀H₁₀₂N₁₄O₂ [ No CAS ]

References: [1]Journal of the Chemical Society. Chemical communications,1995,p. 1921 - 1924.

3
[ 27318-90-7 ]
[ 613-73-0 ]
Naphtho[2,3-f][1,ω]phenanthroline-9,14-dicarbonitrile [ No CAS ]

References: [1]Chemical Communications,1999,p. 1171 - 1172.

4
[ 27318-90-7 ]
[ 7474-78-4 ]
[ 1037676-42-8 ]

References: [1]Tetrahedron,2008,vol. 64,p. 5410 - 5415.

5
[ 27318-90-7 ]
[ 4506-66-5 ]
[ 177528-16-4 ]

References: [1]Tetrahedron Letters,2008,vol. 49,p. 4933 - 4936.

6
[ 27318-90-7 ]
[ 171010-00-7 ]
[ 4506-66-5 ]
[ 171010-12-1 ]

References: [1]Journal of the Chemical Society. Chemical communications,1995,p. 1921 - 1924.

7
[ 27318-90-7 ]
cadmium(II) nitrate tetrhydrate [ No CAS ]
[ 23351-91-9 ]
[Cd(5-bromoisophthalate)(4,5-diazafluoren-9-one)(water)3]*2water [ No CAS ]

References: [1]Polyhedron,2008,vol. 27,p. 2327 - 2336.

8
[ 27318-90-7 ]
cadmium(II) nitrate tetrhydrate [ No CAS ]
[ 23351-91-9 ]
[ 1055875-10-9 ]

References: [1]Polyhedron,2008,vol. 27,p. 2327 - 2336.

9
[ 27318-90-7 ]
cadmium(II) nitrate tetrhydrate [ No CAS ]
[ 23351-91-9 ]
[ 1056148-54-9 ]

References: [1]Polyhedron,2008,vol. 27,p. 2327 - 2336.

10
[ 27318-90-7 ]
cadmium(II) nitrate tetrhydrate [ No CAS ]
[ 23351-91-9 ]
[Cd₂(5-bromoisophthalate)2(1,10-phenanthroline-5,6-dione)2]n*n(water) [ No CAS ]

References: [1]Polyhedron,2008,vol. 27,p. 2327 - 2336.

11
[ 27318-90-7 ]
[ 619-66-9 ]
[ 865169-07-9 ]

Yield	Reaction Conditions	Operation in experiment
75%	With ammonium acetate; glacial acetic acid; for 4h;Reflux; Inert atmosphere;	A mixture of ammonium acetate (3.5g, 45mmol), 4-carboxybenzaldehyde (150mg, 1mmol) 1,10-phenanthroline-5,6-dione (210mg, 1mmol) and glacial acetic acid (40mL) was refluxed for 4h under argon atmosphere. After cooled to room temperature, diluted with amount of water (30mL) and neutralized with concentrated aqueous ammonia. The resulting orange solution was removed to give an orange powder, which was washed with amounts of water and dried under vacuum. Yield: 255mg, 75%. MALDI-TOF-MS (DMSO, m/z): 341.1 ([M+1]+).
67.1%	With ammonium acetate; glacial acetic acid; at 110℃; for 4h;	General procedure: A solution containing 1,10-phenanthroline-5,6-dione (1.6 mmol, 347 mg), substituted benzaldehyde (1.6 mmol), 20 ml of HAc and NH4Ac (33 mmol, 2.53 g), was heated at 110 C under reflux for 4 h. Then, 20 ml of water was added and the pH value was adjusted to 7.0 at room temperature. The solution was filtered and dried in vacuum to obtain a yellow precipitate. The product was purified in a silica gel column by using ethanol as eluent. 1a: yield 78.4%; mp. 217-219 C, ESI-MS (in MeOH): m/z: 219.1, ([M + H]), 438.1,([M + 2H]2+). 2a: yield 79.5%; mp. 226-228 C, ESI-MS (in MeOH): m/z: 339.15, ([M + H]+), 678.1, ([M + 2H]2+). 3a: yield 64.4%; mp. 262-265 C, ESI-MS (in MeOH): m/z: 325.1, ([M + H]+), 650.3, ([M + 2H]2+). 4a: yield 75.7%; mp. 234-236 C, ESI-MS (in MeOH): m/z: 311.1, ([M + H]+). 5a: yield 67.1%; mp. 232-235 C, ESI-MS (in MeOH): m/z: 339.1, ([M + H]+). 6a: yield 67.7%; mp. 280-283 C, ESI-MS (in MeOH): m/z: 363.1, ([M + H]+), 726.1, ([M + 2H]2+). 7a: yield 63.4%; mp. 269-273 C, ESI-MS (in MeOH): m/z: 375.2, ([M + H]+), 750, ([M 2H]2+), 772.8, ([M + H + Na]2+).
63%	With ammonium acetate; glacial acetic acid; for 2h;Reflux;	General procedure: o-TFPIP was prepared by a similar method to that reported [31], and with some modification. In general,a solution of 1,10-phenanthraquinone (525 mg, 2.5 mmol), ammonium acetate (3.88 g, 50 mmol), and2-trifluoridphenylaldehyde (609 mg, 3.5 mmol) in 10 mL of glacial acetic acid was refluxed for 2 h. The cooled deep red solution was diluted with 25 mL of water and neutralized with ammonium hydroxide.Then the mixture was filtered and the precipitates washed with water and acetone, then dried andpurified by chromatography over 60-80 mesh SiO2 using absolute ethanol as eluent. The obtained yield was 516 mg (54%) [32].

	With ammonium acetate; glacial acetic acid; at 100℃; for 0.333333h;Microwave irradiation;	General procedure: Phenanthroimidazole derivatives were synthesized in accordancewith the literature procedure with some modifications. Generally, amixture of 1,10-phenanthroline-5,6-dione (1.50 mmol), benzaldehyde(2.25 mmol), ammonium acetate (51.9 mmol), and glacial acetic acidwas heated at 100 C for 20 min under microwave irradiation (Scheme1). Then, 20 mL of water was added, and the pH value was adjusted to 7.0 at room temperature [47-49]. The solution was filtered and dried ina vacuum to obtain a yellow precipitate. The product was purified in asilica gel column by using ethanol as eluent. The target compoundswere characterized by ESI-MS and 1H- and 13C NMR spectroscopy.
	With ammonium acetate; glacial acetic acid; at 130℃; for 4h;	A cooled mixture of conc. H2SO4-HNO3 (60 mL, 2:1, v/v) was addedwith 1,10-phenanthroline (4 g, 22 mmol) and KBr (4 g, 33 mmol) andstirred at 130 C for 3 h. A yellow solution was cautiously neutralizedwith NaOH solution (10 molL 1) until its pH was neutral. The resultingmixture was extracted with CH2Cl2 and dried with anhydrous Na2SO4.Afterward, solvents were removed, and PDO was obtained as a yellowsolid. Then, PDO (0.420 g, 2 mmol), 4-carboxybenzaldehyde (0.360 g,2.4 mmol), and CH3COONH4 (3.2 g, 41.5 mmol) were mixed in 50 mL ofCH3COOH and stirred at 130 C for 4 h. After being cooled to roomtemperature, the solution was adjusted to pH 5.0 by adding NH3H2O(25 wt%) solution while stirring, and HNCP was dried in vacuum. HNCP(0.34 g, 0.79 mmol), 1,2-diaminobenzene (0.325 g, 3 mmol), 1-hydroxybenzotriazole(HOBT; 0.135 g, 1 mmol), N,Ndicyclohexylcarbodiimide(DCC; 0.248 g, 1.2 mmol), and triethylamine(167 μL) were dissolved in 30 mL of DMF at 4 C for 2 h whilestirring. The resulting mixture was stirred at room temperature for 24 hunder a N2 atmosphere. The faint yellow solid was filtered, washed withCH2Cl2 and Et2OH, and dried in vacuum.

References: [1]Chemical Communications,2020,vol. 56,p. 12130 - 12133.
[2]Chemistry - A European Journal,2011,vol. 17,p. 11743 - 11746.
[3]Inorganic Chemistry,2014,vol. 53,p. 10952 - 10963.
[4]Green Chemistry,2020,vol. 22,p. 1650 - 1661.
[5]Journal of Inorganic Biochemistry,2020,vol. 210.
[6]Chemical Communications,2008,p. 5307 - 5309.
[7]Dalton Transactions,2020,vol. 49,p. 14826 - 14836.
[8]Dalton Transactions,2015,vol. 44,p. 14323 - 14332.
[9]European Journal of Medicinal Chemistry,2013,vol. 63,p. 57 - 63.
[10]Journal of Coordination Chemistry,2016,vol. 69,p. 3507 - 3517.
[11]Bioorganic Chemistry,2019,vol. 88.
[12]Journal of Inorganic Biochemistry,2021,vol. 216.
[13]European Journal of Medicinal Chemistry,2022,vol. 236.

12
[ 25365-71-3 ]
[ 27318-90-7 ]
[ 852147-20-7 ]

Yield	Reaction Conditions	Operation in experiment
58%	With ammonium acetate; In acetic acid; for 1.5h;Reflux;	1.7 g of POCl3 was added drop wise to a solution of 2-phenyindole (1.93 g) in 20 mL of DMF, at 10 C. The mixture was stirred at 50 C. for 1 hr, cooled and diluted with saturated NaHCO3. The suspension was heated at 60 C. for 15 min, cooled, the precipitates of 2-phenylindol-3-carboxaldehyde were filtered. Yield 2.05 g (93%). The mixture of phenanthroquinoline (0.105 g) and 2-phenylindol-3-carboxaldehyde (0.111 g) was refluxed in 3 mL of acetic acid in the presence of 0.39 g of ammonium acetate for 1.5 hrs. The red colored solution was poured in water (100 ml) and washed with DCM (3×40 ml). The aqueous layer was then neutralized with saturated aqueous solution of NA2CO3, the solid obtained was filtered, washed with EtOH and crystallized from DMF: EtOH:H2O=1:1:1. A purified solid 0.12 g was achieved, with a yield of 58%.

References: [1]Patent: US2010/168417,2010,A1 .Location in patent: Page/Page column 32.

13
[ 27318-90-7 ]
[ 42906-19-4 ]
[ 1293911-75-7 ]

References: [1]Chinese Chemical Letters,2011,vol. 22,p. 647 - 650.

14
[ 27318-90-7 ]
[ 99970-84-0 ]
[ 1413925-97-9 ]

References: [1]Transition Metal Chemistry,2012,vol. 37,p. 721 - 726.

15
[ 3314-30-5 ]
[ 27318-90-7 ]
[ 1444124-50-8 ]

Yield	Reaction Conditions	Operation in experiment
	With ammonium acetate; L-proline; In methanol; at 60℃; for 3h;	In a 50 mL round bottom flask 1,10-phenanthroline-5,6-dione (4.7 mmol), 1H-benzimidazole-2-carbaldehyde (5 mmol) and ammonium acetate (10 mmol) were taken in presence of 15 molpercent of L-proline in methanol (20 mL). Then the reaction mixture was stirred at 60 C for 3 h. After completion of the reaction, volume of the reaction mixture was reduced, diluted with water and extracted with ethyl acetate. Organic layer was dried over anhydrous MgSO4 and then solvent was removed under reduced pressure. Crude product was washed with n-hexane and recrystallized from ethanol to obtain the pure product. Anal. Calc. for C20H12N6: C, 71.42; H, 3.59; N, 24.99. Found: C,71.33; H, 3.62; N, 25.05percent;

References: [1]Inorganica Chimica Acta,2013,vol. 402,p. 75 - 82.

16
[ 27318-90-7 ]
[ 4506-66-5 ]
[ 176649-65-3 ]

Yield	Reaction Conditions	Operation in experiment
	With potassium carbonate; In ethanol; water; for 0.666667h;Reflux; Inert atmosphere;	dadppz was synthesized according to modified method [24]. Briefly, a mixture of 1,10-phenanthroline-5,6-dione (0.252 g, 1.2 mM), 1,2,4,5-benzenetetramine tetrahydrochloride (0.341 g, 1.2 mM), and potassium carbonate (0.331 g, 2.4 mM) in ethanol (50mL) and H2O (5 mL) was refluxed under argon for 40 min. After the reaction mixture was allowed to stand at room temperature, the precipitate was filtered and washed with 10 mL ethanol. The filtrate was evaporated under reduced pressure to 5mL. Upon cooling, a red precipitate was obtained by dropwise addition of water. ES-MS (CH3CN, m/z): 313.3 [M + 1]+.

References: [1]Chemistry - A European Journal,2018,vol. 24,p. 5100 - 5111.
[2]Journal of Coordination Chemistry,2013,vol. 66,p. 2423 - 2433.
[3]Transition Metal Chemistry,2013,vol. 38,p. 563 - 571.

17
[ 82413-63-6 ]
[ 27318-90-7 ]
[ 62-53-3 ]
4-(4-(1-phenyl-1H-imidazo[4,5-f ][1,10]phenanthrolin-2-yl)-benzyl)morpholine [ No CAS ]