6′-Bromo-1′H-spiro­[cyclo­hexane-1,2′-pyrido[2,3-d]pyrimidin]-4′(3′H)-one

Yang, L.; Shi, D.; Chen, S.; Chai, H.; Li, J.

doi:10.1107/S1600536811052299

organic compounds

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ISSN: 2056-9890

Volume 68| Part 1| January 2012| Page o178

doi:10.1107/S1600536811052299

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6′-Bromo-1′H-spiro[cyclohexane-1,2′-pyrido[2,3-d]pyrimidin]-4′(3′H)-one

Liupan Yang,^a Daxin Shi,^a Shu Chen,^a Hongxin Chai ^a and Jiarong Li ^a ^*

^aSchool of Chemical Engineering and Environment, Beijing Institue of Technology, Beijing 100081, People's Republic of China
^*Correspondence e-mail: jrli@bit.edu.cn

(Received 31 October 2011; accepted 4 December 2011; online 21 December 2011)

The title compound, C₁₂H₁₄BrN₃O, is built up from two fused six-membered rings and one six-membered ring linked through a spiro C atom. The hydropyrimidine ring has an envelope conformation and the cyclohexane ring is in a chair conformation. In the crystal, molecules are linked by N—H⋯O and N—H⋯N hydrogen bonds, forming a molecular tape along the b axis.

Related literature

For medicinal and biological properties of 2,3-dihydropyrido[2,3-d]-pyrimidin-4(1H)-one derivatives, see: Parish et al. (1982 ); Narayana et al. (2009 ). For related structures, see: Shi et al. (2010 ); Ling et al. (2009 ).

Experimental

Crystal data

C₁₂H₁₄BrN₃O
M_r = 296.17
Monoclinic, P 2₁ /c
a = 10.591 (3) Å
b = 12.359 (3) Å
c = 9.116 (3) Å
β = 97.951 (4)°
V = 1181.7 (6) Å³
Z = 4
Mo Kα radiation
μ = 3.47 mm⁻¹
T = 153 K
0.40 × 0.24 × 0.09 mm

Data collection

Rigaku AFC10/Saturn724+ diffractometer
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009 ) T_min = 0.324, T_max = 0.732
10128 measured reflections
3160 independent reflections
2283 reflections with I > 2σ(I)
R_int = 0.046

Refinement

R[F² > 2σ(F²)] = 0.035
wR(F²) = 0.074
S = 1.00
3160 reflections
162 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.55 e Å⁻³
Δρ_min = −0.66 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯N3ⁱ	0.83 (2)	2.52 (2)	3.337 (2)	169 (2)
N2—H2N⋯O1ⁱⁱ	0.83 (2)	1.98 (2)	2.807 (2)	175 (2)
Symmetry codes: (i) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: CrystalClear (Rigaku/MSC, 2009); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: CrystalStructure (Rigaku/MSC, 2009); software used to prepare material for publication: CrystalStructure.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811052299/is5001sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536811052299/is5001Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536811052299/is5001Isup3.cml

checkCIF report

Comment top

2,3-Dihydropyrido[2,3-d]-pyrimidin-4(1H)-ones are a class of fused heterocycles which possess diuretic (Parish et al., 1982) and anti-bacterial activity (Narayana et al., 2009). 2-Substituted 2,3-dihydropyrido [2,3-d]pyrimidin-4(1H)-one derivatives can be obtained from the cyclocondensation of 2-amino-3-cyanopyridine with cyclopentanone (Shi et al., 2010). Here, we report the crystal structure of the title compound (Fig. 1). The molecular structure is built up with two fused six-membered ring and one six-membered ring linked through a spiro C atom. The pyrimidine ring has an envelope conformation, similar to that found in spiro{cyclopentane- 1,2'(1'H)pyrido[2',3'-d]pyrimidin-4'(3'H)-one} (Shi et al., 2010). Cyclohexane ring has a similar chair conformation as cyclohexanespiro-2'-[2',3',6',7'-tetrahydro-1'H- cyclopenta[d]pyrimidin]-4'(5'H)-one (Ling et al., 2009). The crystal packing (Fig. 2) is stabilized by intermolecular N—H···O and N—H···N hydrogen bonds (Table 1).

Related literature top

For medicinal and biological properties of 2,3-dihydropyrido[2,3-d]-pyrimidin-4(1H)-one derivatives, see: Parish et al. (1982); Narayana et al. (2009). For related structures, see: Shi et al. (2010); Ling et al. (2009).

Experimental top

A solution of 5-Br-2-amino-3-cyanopyridine (2 mmol) and sodium methylate (0.6 mmol) was refluxed in cyclohexanone (3 ml) for 10 min. The reaction mixture was cooled to room temperature and then filtered to give the title compound. The product was recrystallizated from THF to give light yellow crystalline powder (m.p. 531–532 K). ¹H–NMR(DMSO, p.p.m.):1.30–1.73 (10H, m, C₅H₁₀), 7.79 (1H, s, NH), 7.92 (1H, d, J = 2.4 Hz, Pyridine-H), 8.24 (1H, d, J = 2.4 Hz, Pyridine-H), 8.35 (1H, s, NH); ESI-MS m/z: [M+H]⁺ 296.1; C₁₂H₁₄BrN₃O: calcd. C 48.67, H 4.76, N 14.19; found C 48.88, H 4.787, N 14.06.

Computing details top

Data collection: CrystalClear (Rigaku/MSC, 2009); cell refinement: CrystalClear (Rigaku/MSC, 2009); data reduction: CrystalClear (Rigaku/MSC, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: CrystalStructure (Rigaku/MSC, 2009); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 30% probability level.
	Fig. 2. A packing diagram, showing N—H···O and N—H···N interactions (dotted lines) in the crystal structure of the title compound.

6'-Bromo-1'H-spiro[cyclohexane-1,2'-pyrido[2,3- d]pyrimidin]-4'(3'H)-one top

Crystal data top

C₁₂H₁₄BrN₃O	F(000) = 600
M_r = 296.17	D_x = 1.665 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 3621 reflections
a = 10.591 (3) Å	θ = 2.6–29.1°
b = 12.359 (3) Å	µ = 3.47 mm⁻¹
c = 9.116 (3) Å	T = 153 K
β = 97.951 (4)°	Platelet, colourless
V = 1181.7 (6) Å³	0.40 × 0.24 × 0.09 mm
Z = 4

Data collection top

Rigaku AFC10/Saturn724+ diffractometer	3160 independent reflections
Radiation source: Rotating Anode	2283 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.046
Detector resolution: 28.5714 pixels mm^-1	θ_max = 29.1°, θ_min = 2.6°
ϕ and ω scans	h = −14→12
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009)	k = −16→16
T_min = 0.324, T_max = 0.732	l = −12→12
10128 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.035	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.074	H atoms treated by a mixture of independent and constrained refinement
S = 1.00	w = 1/[σ²(F_o²) + (0.0295P)² + 0.126P] where P = (F_o² + 2F_c²)/3
3160 reflections	(Δ/σ)_max = 0.001
162 parameters	Δρ_max = 0.55 e Å⁻³
0 restraints	Δρ_min = −0.66 e Å⁻³

Crystal data top

C₁₂H₁₄BrN₃O	V = 1181.7 (6) Å³
M_r = 296.17	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 10.591 (3) Å	µ = 3.47 mm⁻¹
b = 12.359 (3) Å	T = 153 K
c = 9.116 (3) Å	0.40 × 0.24 × 0.09 mm
β = 97.951 (4)°

Data collection top

Rigaku AFC10/Saturn724+ diffractometer	3160 independent reflections
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2009)	2283 reflections with I > 2σ(I)
T_min = 0.324, T_max = 0.732	R_int = 0.046
10128 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.035	0 restraints
wR(F²) = 0.074	H atoms treated by a mixture of independent and constrained refinement
S = 1.00	Δρ_max = 0.55 e Å⁻³
3160 reflections	Δρ_min = −0.66 e Å⁻³
162 parameters

Special details top

Experimental. Spectral data: IR (KBr): 3274, 3175, 2927, 1677, 1610, 1422 cm^-1.

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Br1	0.99820 (2)	0.65490 (2)	0.61599 (3)	0.03640 (10)
O1	0.58435 (14)	0.40734 (11)	0.39085 (16)	0.0171 (3)
N1	0.45035 (17)	0.52063 (14)	0.2500 (2)	0.0151 (4)
N2	0.49356 (17)	0.71034 (14)	0.2458 (2)	0.0188 (4)
N3	0.68151 (16)	0.78374 (13)	0.3597 (2)	0.0176 (4)
C1	0.2735 (2)	0.64979 (16)	0.2411 (2)	0.0150 (4)
H1A	0.2814	0.6418	0.3501	0.018*
H1B	0.2496	0.7257	0.2164	0.018*
C2	0.1676 (2)	0.57477 (17)	0.1687 (2)	0.0179 (5)
H2A	0.1865	0.4994	0.2015	0.021*
H2B	0.0855	0.5960	0.2005	0.021*
C3	0.1565 (2)	0.58081 (18)	−0.0002 (2)	0.0194 (5)
H3A	0.0902	0.5296	−0.0448	0.023*
H3B	0.1303	0.6547	−0.0336	0.023*
C4	0.2831 (2)	0.55308 (17)	−0.0524 (2)	0.0172 (5)
H4A	0.2751	0.5617	−0.1613	0.021*
H4B	0.3046	0.4765	−0.0285	0.021*
C5	0.3902 (2)	0.62565 (16)	0.0209 (2)	0.0160 (4)
H5A	0.3743	0.7006	−0.0152	0.019*
H5B	0.4717	0.6014	−0.0098	0.019*
C6	0.40340 (19)	0.62564 (15)	0.1905 (2)	0.0129 (4)
C7	0.55747 (19)	0.49967 (15)	0.3433 (2)	0.0127 (4)
C8	0.64262 (19)	0.59204 (16)	0.3832 (2)	0.0125 (4)
C9	0.6063 (2)	0.69577 (16)	0.3293 (2)	0.0139 (4)
C10	0.7594 (2)	0.57798 (17)	0.4683 (2)	0.0174 (5)
H10	0.7863	0.5086	0.5051	0.021*
C11	0.8365 (2)	0.66793 (17)	0.4987 (3)	0.0203 (5)
C12	0.7942 (2)	0.76778 (17)	0.4435 (3)	0.0203 (5)
H12	0.8482	0.8286	0.4665	0.024*
H1N	0.408 (2)	0.4668 (17)	0.220 (2)	0.015 (6)*
H2N	0.474 (2)	0.7700 (19)	0.208 (3)	0.026 (7)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Br1	0.02057 (13)	0.02781 (14)	0.05373 (19)	−0.00860 (11)	−0.01997 (11)	0.01191 (13)
O1	0.0199 (8)	0.0096 (7)	0.0194 (8)	0.0000 (6)	−0.0054 (6)	0.0021 (6)
N1	0.0143 (9)	0.0080 (8)	0.0209 (10)	−0.0027 (7)	−0.0049 (7)	−0.0002 (7)
N2	0.0163 (10)	0.0070 (9)	0.0298 (11)	−0.0006 (7)	−0.0085 (8)	0.0047 (8)
N3	0.0143 (10)	0.0111 (9)	0.0259 (11)	−0.0045 (7)	−0.0027 (8)	0.0016 (8)
C1	0.0165 (11)	0.0128 (10)	0.0153 (10)	0.0017 (9)	0.0011 (8)	−0.0012 (8)
C2	0.0133 (11)	0.0189 (11)	0.0216 (12)	−0.0025 (9)	0.0031 (9)	−0.0022 (9)
C3	0.0130 (11)	0.0208 (11)	0.0227 (12)	−0.0036 (9)	−0.0029 (9)	−0.0027 (10)
C4	0.0194 (11)	0.0184 (10)	0.0131 (10)	0.0000 (9)	−0.0003 (8)	−0.0017 (9)
C5	0.0167 (11)	0.0145 (10)	0.0175 (11)	0.0032 (8)	0.0050 (9)	0.0026 (9)
C6	0.0117 (10)	0.0070 (9)	0.0182 (11)	0.0004 (8)	−0.0042 (8)	0.0004 (8)
C7	0.0135 (10)	0.0112 (10)	0.0132 (10)	0.0009 (8)	0.0013 (8)	−0.0005 (8)
C8	0.0129 (10)	0.0113 (10)	0.0130 (10)	−0.0002 (8)	0.0006 (8)	−0.0005 (8)
C9	0.0137 (10)	0.0111 (9)	0.0165 (11)	−0.0006 (8)	0.0010 (8)	−0.0003 (8)
C10	0.0153 (11)	0.0151 (10)	0.0204 (11)	−0.0008 (9)	−0.0020 (9)	0.0041 (9)
C11	0.0120 (10)	0.0200 (11)	0.0262 (12)	−0.0040 (9)	−0.0064 (9)	0.0027 (10)
C12	0.0161 (11)	0.0148 (10)	0.0281 (13)	−0.0052 (9)	−0.0034 (9)	−0.0019 (10)

Geometric parameters (Å, º) top

Br1—C11	1.896 (2)	C3—C4	1.523 (3)
O1—C7	1.240 (2)	C3—H3A	0.9900
N1—C7	1.346 (2)	C3—H3B	0.9900
N1—C6	1.467 (2)	C4—C5	1.525 (3)
N1—H1N	0.83 (2)	C4—H4A	0.9900
N2—C9	1.336 (3)	C4—H4B	0.9900
N2—C6	1.459 (3)	C5—C6	1.533 (3)
N2—H2N	0.83 (2)	C5—H5A	0.9900
N3—C12	1.339 (3)	C5—H5B	0.9900
N3—C9	1.354 (3)	C7—C8	1.469 (3)
C1—C2	1.533 (3)	C8—C10	1.377 (3)
C1—C6	1.539 (3)	C8—C9	1.407 (3)
C1—H1A	0.9900	C10—C11	1.384 (3)
C1—H1B	0.9900	C10—H10	0.9500
C2—C3	1.530 (3)	C11—C12	1.384 (3)
C2—H2A	0.9900	C12—H12	0.9500
C2—H2B	0.9900

C7—N1—C6	128.11 (17)	C4—C5—C6	113.60 (18)
C7—N1—H1N	115.1 (15)	C4—C5—H5A	108.8
C6—N1—H1N	116.7 (15)	C6—C5—H5A	108.8
C9—N2—C6	126.21 (17)	C4—C5—H5B	108.8
C9—N2—H2N	120.3 (17)	C6—C5—H5B	108.8
C6—N2—H2N	112.6 (17)	H5A—C5—H5B	107.7
C12—N3—C9	116.82 (17)	N2—C6—N1	109.55 (16)
C2—C1—C6	112.62 (16)	N2—C6—C5	108.24 (17)
C2—C1—H1A	109.1	N1—C6—C5	110.62 (17)
C6—C1—H1A	109.1	N2—C6—C1	109.04 (16)
C2—C1—H1B	109.1	N1—C6—C1	109.38 (17)
C6—C1—H1B	109.1	C5—C6—C1	109.98 (16)
H1A—C1—H1B	107.8	O1—C7—N1	122.07 (18)
C3—C2—C1	110.73 (17)	O1—C7—C8	121.69 (18)
C3—C2—H2A	109.5	N1—C7—C8	116.22 (17)
C1—C2—H2A	109.5	C10—C8—C9	119.49 (18)
C3—C2—H2B	109.5	C10—C8—C7	120.94 (18)
C1—C2—H2B	109.5	C9—C8—C7	119.53 (18)
H2A—C2—H2B	108.1	N2—C9—N3	117.56 (18)
C4—C3—C2	110.80 (17)	N2—C9—C8	120.06 (18)
C4—C3—H3A	109.5	N3—C9—C8	122.37 (18)
C2—C3—H3A	109.5	C8—C10—C11	118.05 (19)
C4—C3—H3B	109.5	C8—C10—H10	121.0
C2—C3—H3B	109.5	C11—C10—H10	121.0
H3A—C3—H3B	108.1	C12—C11—C10	119.4 (2)
C3—C4—C5	111.35 (17)	C12—C11—Br1	120.17 (16)
C3—C4—H4A	109.4	C10—C11—Br1	120.42 (16)
C5—C4—H4A	109.4	N3—C12—C11	123.84 (19)
C3—C4—H4B	109.4	N3—C12—H12	118.1
C5—C4—H4B	109.4	C11—C12—H12	118.1
H4A—C4—H4B	108.0

C6—C1—C2—C3	−56.1 (2)	N1—C7—C8—C10	−174.77 (19)
C1—C2—C3—C4	56.8 (2)	O1—C7—C8—C9	−178.41 (19)
C2—C3—C4—C5	−55.7 (2)	N1—C7—C8—C9	3.0 (3)
C3—C4—C5—C6	54.2 (2)	C6—N2—C9—N3	174.7 (2)
C9—N2—C6—N1	4.4 (3)	C6—N2—C9—C8	−5.9 (3)
C9—N2—C6—C5	−116.3 (2)	C12—N3—C9—N2	180.0 (2)
C9—N2—C6—C1	124.1 (2)	C12—N3—C9—C8	0.6 (3)
C7—N1—C6—N2	1.1 (3)	C10—C8—C9—N2	179.6 (2)
C7—N1—C6—C5	120.3 (2)	C7—C8—C9—N2	1.8 (3)
C7—N1—C6—C1	−118.4 (2)	C10—C8—C9—N3	−1.0 (3)
C4—C5—C6—N2	−170.86 (16)	C7—C8—C9—N3	−178.8 (2)
C4—C5—C6—N1	69.1 (2)	C9—C8—C10—C11	0.6 (3)
C4—C5—C6—C1	−51.8 (2)	C7—C8—C10—C11	178.3 (2)
C2—C1—C6—N2	171.29 (17)	C8—C10—C11—C12	0.2 (3)
C2—C1—C6—N1	−68.9 (2)	C8—C10—C11—Br1	179.67 (16)
C2—C1—C6—C5	52.7 (2)	C9—N3—C12—C11	0.3 (3)
C6—N1—C7—O1	176.9 (2)	C10—C11—C12—N3	−0.6 (4)
C6—N1—C7—C8	−4.5 (3)	Br1—C11—C12—N3	179.88 (18)
O1—C7—C8—C10	3.8 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···N3ⁱ	0.83 (2)	2.52 (2)	3.337 (2)	169 (2)
N2—H2N···O1ⁱⁱ	0.83 (2)	1.98 (2)	2.807 (2)	175 (2)

Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) −x+1, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₂H₁₄BrN₃O
M_r	296.17
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	153
a, b, c (Å)	10.591 (3), 12.359 (3), 9.116 (3)
β (°)	97.951 (4)
V (Å³)	1181.7 (6)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	3.47
Crystal size (mm)	0.40 × 0.24 × 0.09

Data collection
Diffractometer	Rigaku AFC10/Saturn724+ diffractometer
Absorption correction	Multi-scan (CrystalClear; Rigaku/MSC, 2009)
T_min, T_max	0.324, 0.732
No. of measured, independent and observed [I > 2σ(I)] reflections	10128, 3160, 2283
R_int	0.046
(sin θ/λ)_max (Å⁻¹)	0.684

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.035, 0.074, 1.00
No. of reflections	3160
No. of parameters	162
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.55, −0.66

Computer programs: CrystalClear (Rigaku/MSC, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), CrystalStructure (Rigaku/MSC, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···N3ⁱ	0.83 (2)	2.52 (2)	3.337 (2)	169 (2)
N2—H2N···O1ⁱⁱ	0.83 (2)	1.98 (2)	2.807 (2)	175 (2)

Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) −x+1, y+1/2, −z+1/2.

Acknowledgements

The authors thank Beijing Institute of Technology for the X-ray diffraction analysis.

References

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