Literature DB >> 22199876

(2R)-4-[(9H-Fluoren-9-ylmeth-oxy)carbon-yl]-2-methyl-piperazin-1-ium chloride.

Anne Ertan, Parhalad Sharma, Dokka Nagaraju, K Deepthi, Sulur G Manjunatha.   

Abstract

The synthesis of the title salt, C(20)H(23)N(2)O(2) (+)·Cl(-), was carried out with a precursor of known absolute configuration (R) and the X-ray analysis confirmed that the product retained the absolute configuration. In the crystal, the dominant packing motif is a chain running along [010] generated by N-H⋯Cl hydrogen bonding. C-H⋯O and C-H⋯Cl inter-actions are also observed.

Entities:  

Year:  2011        PMID: 22199876      PMCID: PMC3239028          DOI: 10.1107/S1600536811048306

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the use of piperazine and substituted piperazines as good linkers to pharmacophores in attempts to obtain compounds with desired pharmacokinetic and pharmacological properties, see: Cho et al. (2010 ▶); Wang et al. (2009 ▶). For packing coefficients, see: Kitaigorodskij (1973 ▶).

Experimental

Crystal data

C20H23N2O2 +·Cl− M = 358.85 Monoclinic, a = 8.3492 (3) Å b = 7.4954 (2) Å c = 14.9246 (3) Å β = 90.6740 (18)° V = 933.93 (5) Å3 Z = 2 Mo Kα radiation μ = 0.22 mm−1 T = 293 K 0.28 × 0.20 × 0.08 mm

Data collection

Nonius KappaCCD diffractometer 4227 measured reflections 4221 independent reflections 3684 reflections with I > 2σ(I) R int = 0.022

Refinement

R[F 2 > 2σ(F 2)] = 0.036 wR(F 2) = 0.086 S = 1.03 4221 reflections 227 parameters 1 restraint H-atom parameters constrained Δρmax = 0.16 e Å−3 Δρmin = −0.15 e Å−3 Absolute structure: Flack (1983 ▶), 1922 Friedel pairs Flack parameter: −0.04 (5) Data collection: COLLECT (Nonius, 1998 ▶); cell refinement: SCALEPACK (Otwinowski & Minor, 1997 ▶); data reduction: DENZO (Otwinowski & Minor, 1997 ▶) and SCALEPACK; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: initial refinement: maXus (MacKay et al., 2000 ▶); final refinement: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: PLATON (Spek, 2009 ▶) and ORTEPII (Johnson, 1976 ▶); software used to prepare material for publication: PLATON and ACD/Labs (ACD, 2011 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811048306/kp2361sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811048306/kp2361Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536811048306/kp2361Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C20H23N2O2+·ClF(000) = 380
Mr = 358.85Dx = 1.276 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 2263 reflections
a = 8.3492 (3) Åθ = 1.0–27.5°
b = 7.4954 (2) ŵ = 0.22 mm1
c = 14.9246 (3) ÅT = 293 K
β = 90.6740 (18)°Block, colourless
V = 933.93 (5) Å30.28 × 0.20 × 0.08 mm
Z = 2
Nonius KappaCCD diffractometer3684 reflections with I > 2σ(I)
Radiation source: fine-focusRint = 0.022
graphiteθmax = 27.5°, θmin = 3.0°
φ and ω scans with κ offsetsh = −10→10
4227 measured reflectionsk = −9→9
4221 independent reflectionsl = −19→19
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.036w = 1/[σ2(Fo2) + (0.037P)2 + 0.176P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.086(Δ/σ)max < 0.001
S = 1.03Δρmax = 0.16 e Å3
4221 reflectionsΔρmin = −0.15 e Å3
227 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), FC*=KFC[1+0.001XFC2Λ3/SIN(2Θ)]-1/4
1 restraintExtinction coefficient: 0.075 (4)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 1922 Friedel pairs
Secondary atom site location: difference Fourier mapFlack parameter: −0.04 (5)
Experimental. Crystals were crystallized from methanol/heptane by vapour diffusion.Number of collected frames: 212 Number of repeats: 1 Crystal-Detector distance (mm): 30 Exposure time (sec) per frame: 5 Phi-rotation (°) step: 2
Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles
Refinement. Refinement on F2 for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The observed criterion of F2 > σ(F2) is used only for calculating -R-factor-obs 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.
xyzUiso*/Ueq
O80.44893 (17)0.0878 (2)0.65110 (9)0.0556 (5)
O90.61979 (15)0.06962 (17)0.76938 (8)0.0404 (4)
N10.86676 (19)−0.2463 (2)0.55195 (9)0.0431 (5)
N40.61615 (18)−0.1517 (3)0.66869 (10)0.0468 (5)
C20.7114 (2)−0.1768 (3)0.51533 (12)0.0512 (6)
C30.5787 (2)−0.2213 (3)0.57921 (13)0.0540 (7)
C50.7678 (2)−0.2172 (3)0.70499 (11)0.0438 (6)
C60.9062 (2)−0.1750 (3)0.64313 (11)0.0397 (5)
C71.0634 (2)−0.2547 (3)0.67673 (14)0.0532 (7)
C80.5532 (2)0.0098 (3)0.69198 (11)0.0398 (5)
C100.5939 (2)0.2555 (2)0.78753 (11)0.0380 (5)
C110.70593 (19)0.3087 (2)0.86403 (10)0.0336 (5)
C120.6628 (2)0.2475 (2)0.95797 (11)0.0358 (5)
C130.5230 (2)0.2774 (3)1.00485 (13)0.0446 (6)
C140.5175 (3)0.2224 (3)1.09407 (13)0.0529 (7)
C150.6472 (3)0.1385 (3)1.13435 (13)0.0571 (7)
C160.7860 (3)0.1070 (3)1.08760 (13)0.0514 (7)
C170.7936 (2)0.1632 (2)0.99900 (11)0.0389 (5)
C180.9257 (2)0.1579 (2)0.93493 (11)0.0370 (5)
C191.0795 (2)0.0892 (3)0.94323 (15)0.0504 (7)
C201.1808 (2)0.0990 (3)0.87068 (16)0.0555 (7)
C211.1300 (2)0.1765 (3)0.79113 (15)0.0528 (7)
C220.9768 (2)0.2495 (3)0.78302 (12)0.0429 (5)
C230.87605 (19)0.2402 (2)0.85559 (11)0.0349 (5)
Cl10.82783 (6)0.33785 (7)0.55846 (3)0.0512 (2)
H1A0.95740−0.205300.507000.0520*
H1B0.86370−0.363700.549000.0520*
H2A0.71940−0.049500.509400.0620*
H2B0.68890−0.228700.457700.0620*
H3A0.56490−0.348400.581300.0650*
H3B0.48160−0.166700.557700.0650*
H5A0.78820−0.161000.761800.0520*
H5B0.76240−0.344200.713000.0520*
H60.91990−0.048000.639700.0480*
H7A1.08780−0.207800.735200.0640*
H7B1.14880−0.226500.636700.0640*
H7C1.05130−0.381900.680400.0640*
H10A0.615300.325200.735100.0460*
H10B0.484600.272500.804900.0460*
H110.710900.453000.857700.0400*
H130.434800.335400.975100.0540*
H140.422000.240301.128200.0640*
H150.641900.101801.195900.0690*
H160.875200.048801.116400.0620*
H191.112800.038800.999600.0610*
H201.286900.049800.873900.0670*
H211.204900.175600.741200.0630*
H220.943200.309100.729000.0510*
U11U22U33U12U13U23
O80.0442 (8)0.0714 (10)0.0508 (7)0.0151 (7)−0.0161 (6)−0.0121 (7)
O90.0444 (7)0.0403 (7)0.0363 (6)0.0044 (6)−0.0068 (5)−0.0027 (5)
N10.0498 (9)0.0414 (8)0.0382 (8)−0.0015 (7)0.0020 (6)−0.0056 (7)
N40.0417 (8)0.0550 (9)0.0435 (8)0.0051 (8)−0.0024 (6)−0.0121 (8)
C20.0568 (12)0.0583 (12)0.0383 (8)0.0044 (10)−0.0124 (8)−0.0084 (9)
C30.0476 (11)0.0600 (13)0.0542 (11)0.0000 (9)−0.0064 (9)−0.0203 (10)
C50.0476 (10)0.0462 (12)0.0375 (9)0.0095 (8)0.0009 (7)−0.0003 (7)
C60.0433 (9)0.0379 (9)0.0378 (8)0.0011 (8)−0.0045 (7)−0.0016 (8)
C70.0459 (11)0.0595 (12)0.0541 (11)0.0070 (10)−0.0048 (9)0.0006 (10)
C80.0344 (9)0.0496 (11)0.0355 (8)−0.0001 (8)0.0007 (7)−0.0041 (8)
C100.0345 (9)0.0386 (9)0.0407 (9)0.0062 (7)−0.0036 (7)−0.0001 (8)
C110.0320 (8)0.0346 (10)0.0340 (8)0.0027 (7)−0.0021 (6)−0.0003 (6)
C120.0392 (9)0.0299 (8)0.0384 (8)−0.0017 (7)0.0004 (7)−0.0035 (7)
C130.0439 (10)0.0404 (10)0.0497 (10)−0.0027 (8)0.0080 (8)−0.0064 (8)
C140.0638 (13)0.0478 (12)0.0476 (11)−0.0169 (10)0.0196 (9)−0.0120 (9)
C150.0811 (16)0.0547 (13)0.0357 (9)−0.0228 (12)0.0046 (10)0.0017 (9)
C160.0641 (13)0.0472 (12)0.0425 (10)−0.0114 (10)−0.0101 (9)0.0081 (8)
C170.0441 (10)0.0325 (8)0.0399 (9)−0.0059 (7)−0.0046 (7)0.0014 (7)
C180.0365 (9)0.0302 (8)0.0440 (9)0.0007 (7)−0.0061 (7)−0.0009 (7)
C190.0427 (11)0.0424 (11)0.0659 (12)0.0049 (9)−0.0119 (9)0.0038 (9)
C200.0333 (10)0.0463 (12)0.0866 (16)0.0063 (9)−0.0055 (10)−0.0070 (11)
C210.0379 (10)0.0565 (12)0.0641 (13)−0.0028 (9)0.0104 (9)−0.0160 (10)
C220.0392 (9)0.0469 (10)0.0425 (9)−0.0032 (8)0.0013 (7)−0.0044 (8)
C230.0323 (8)0.0325 (8)0.0397 (8)0.0004 (7)−0.0030 (6)−0.0025 (7)
Cl10.0585 (3)0.0495 (3)0.0457 (2)0.0006 (2)0.0055 (2)−0.0020 (2)
O8—C81.208 (2)C19—C201.384 (3)
O9—C81.353 (2)C20—C211.384 (3)
O9—C101.436 (2)C21—C221.395 (3)
N1—C21.495 (2)C22—C231.381 (2)
N1—C61.495 (2)C2—H2A0.9600
N4—C31.464 (3)C2—H2B0.9600
N4—C51.457 (2)C3—H3A0.9600
N4—C81.366 (3)C3—H3B0.9600
N1—H1A1.0600C5—H5A0.9600
N1—H1B0.8800C5—H5B0.9600
C2—C31.508 (3)C6—H60.9600
C5—C61.521 (2)C7—H7A0.9600
C6—C71.522 (3)C7—H7B0.9600
C10—C111.521 (2)C7—H7C0.9600
C11—C231.517 (2)C10—H10A0.9600
C11—C121.522 (2)C10—H10B0.9600
C12—C171.397 (2)C11—H111.0900
C12—C131.386 (2)C13—H130.9600
C13—C141.395 (3)C14—H140.9600
C14—C151.384 (3)C15—H150.9600
C15—C161.380 (3)C16—H160.9600
C16—C171.390 (3)C19—H190.9600
C17—C181.469 (2)C20—H200.9600
C18—C231.394 (2)C21—H210.9800
C18—C191.388 (2)C22—H220.9600
Cl1···N1i3.1353 (16)H1B···H3A2.5500
Cl1···C223.6222 (19)H2A···H62.5500
Cl1···N1ii3.1167 (16)H2A···Cl13.1300
Cl1···H2A3.1300H2B···O8vii2.4100
Cl1···H222.7200H3A···H1B2.5500
Cl1···H1Bi2.2600H3A···H5B2.5500
Cl1···H1Aii2.0800H3B···O82.3800
Cl1···H7Bii2.9600H3B···Cl1vii3.0900
Cl1···H3Biii3.0900H5A···H14x2.5300
O8···C2iii3.316 (2)H5A···H7A2.5600
O9···C223.276 (2)H5A···O92.2300
O8···H10B2.6900H5B···H7C2.4800
O8···H2Biii2.4100H5B···H3A2.5500
O8···H21iv2.5400H6···H2A2.5500
O8···H10A2.5700H7A···H5A2.5600
O8···H3B2.3800H7A···C213.0200
O9···H5A2.2300H7B···H1A2.5000
N1···N42.829 (2)H7B···Cl1v2.9600
N1···Cl1v3.1167 (16)H7C···H1B2.5000
N1···Cl1vi3.1353 (16)H7C···H5B2.4800
N4···N12.829 (2)H7C···H22vi2.5900
C2···O8vii3.316 (2)H10A···O82.5700
C17···C19viii3.470 (3)H10B···O82.6900
C19···C17ix3.470 (3)H10B···C21iv3.0500
C22···O93.276 (2)H10B···H20iv2.5700
C22···Cl13.6222 (19)H10B···C15xii3.1000
C5···H14x2.9800H10B···C133.0000
C10···H223.0800H10B···C20iv3.0200
C11···H19viii3.0600H11···C14xii2.8700
C12···H19viii2.9400H11···H14xii2.4300
C13···H10B3.0000H13···C16xii2.8900
C14···H20viii2.9800H13···C15xii2.8800
C14···H11x2.8700H14···H5Axii2.5300
C15···H13x2.8800H14···H11x2.4300
C15···H10Bx3.1000H14···C5xii2.9800
C16···H13x2.8900H16···C22ix2.9600
C16···H193.0800H19···C11ix3.0600
C17···H19viii2.9200H19···C12ix2.9400
C18···H19viii3.0400H19···C163.0800
C20···H10Bxi3.0200H19···C18ix3.0400
C21···H10Bxi3.0500H19···C17ix2.9200
C21···H7A3.0200H20···C14ix2.9800
C22···H16viii2.9600H20···H10Bxi2.5700
H1A···Cl1v2.0800H21···O8xi2.5400
H1A···H7B2.5000H22···H7Ci2.5900
H1B···H7C2.5000H22···Cl12.7200
H1B···Cl1vi2.2600H22···C103.0800
C8—O9—C10114.92 (14)C3—C2—H2B110.00
C2—N1—C6112.89 (14)H2A—C2—H2B109.00
C3—N4—C5113.24 (16)N4—C3—H3A110.00
C3—N4—C8117.98 (16)N4—C3—H3B109.00
C5—N4—C8122.64 (17)C2—C3—H3A109.00
C2—N1—H1B108.00C2—C3—H3B109.00
C6—N1—H1A109.00H3A—C3—H3B109.00
C2—N1—H1A107.00N4—C5—H5A109.00
H1A—N1—H1B106.00N4—C5—H5B110.00
C6—N1—H1B114.00C6—C5—H5A108.00
N1—C2—C3109.43 (15)C6—C5—H5B109.00
N4—C3—C2110.33 (15)H5A—C5—H5B109.00
N4—C5—C6111.56 (15)N1—C6—H6109.00
C5—C6—C7112.14 (15)C5—C6—H6109.00
N1—C6—C5108.51 (14)C7—C6—H6108.00
N1—C6—C7109.85 (16)C6—C7—H7A109.00
O9—C8—N4110.82 (15)C6—C7—H7B111.00
O8—C8—O9123.88 (19)C6—C7—H7C109.00
O8—C8—N4125.26 (17)H7A—C7—H7B110.00
O9—C10—C11107.66 (13)H7A—C7—H7C109.00
C10—C11—C12117.54 (13)H7B—C7—H7C109.00
C12—C11—C23101.91 (12)O9—C10—H10A110.00
C10—C11—C23114.66 (13)O9—C10—H10B109.00
C11—C12—C13128.75 (15)C11—C10—H10A111.00
C13—C12—C17120.70 (16)C11—C10—H10B110.00
C11—C12—C17110.36 (14)H10A—C10—H10B110.00
C12—C13—C14118.12 (18)C10—C11—H11103.00
C13—C14—C15121.0 (2)C12—C11—H11113.00
C14—C15—C16121.04 (19)C23—C11—H11107.00
C15—C16—C17118.5 (2)C12—C13—H13119.00
C12—C17—C16120.66 (17)C14—C13—H13123.00
C16—C17—C18130.86 (17)C13—C14—H14120.00
C12—C17—C18108.42 (14)C15—C14—H14119.00
C17—C18—C23108.85 (14)C14—C15—H15120.00
C19—C18—C23120.38 (16)C16—C15—H15119.00
C17—C18—C19130.77 (16)C15—C16—H16120.00
C18—C19—C20118.94 (19)C17—C16—H16121.00
C19—C20—C21120.64 (17)C18—C19—H19119.00
C20—C21—C22120.70 (18)C20—C19—H19122.00
C21—C22—C23118.58 (17)C19—C20—H20121.00
C11—C23—C22128.88 (15)C21—C20—H20119.00
C18—C23—C22120.72 (15)C20—C21—H21117.00
C11—C23—C18110.40 (14)C22—C21—H21122.00
N1—C2—H2A109.00C21—C22—H22121.00
N1—C2—H2B110.00C23—C22—H22120.00
C3—C2—H2A109.00
C10—O9—C8—O8−17.4 (2)C11—C12—C13—C14−173.75 (18)
C10—O9—C8—N4164.52 (14)C17—C12—C13—C140.6 (3)
C8—O9—C10—C11−167.41 (13)C11—C12—C17—C16175.50 (16)
C6—N1—C2—C3−57.2 (2)C11—C12—C17—C18−2.04 (17)
C2—N1—C6—C555.8 (2)C13—C12—C17—C160.2 (3)
C2—N1—C6—C7178.70 (16)C13—C12—C17—C18−177.31 (16)
C5—N4—C3—C2−57.0 (2)C12—C13—C14—C15−0.7 (3)
C8—N4—C3—C296.2 (2)C13—C14—C15—C160.1 (3)
C3—N4—C5—C656.7 (2)C14—C15—C16—C170.7 (3)
C8—N4—C5—C6−95.1 (2)C15—C16—C17—C12−0.8 (3)
C3—N4—C8—O812.5 (3)C15—C16—C17—C18176.07 (18)
C3—N4—C8—O9−169.49 (15)C12—C17—C18—C19179.93 (18)
C5—N4—C8—O8163.05 (18)C12—C17—C18—C230.59 (18)
C5—N4—C8—O9−19.0 (2)C16—C17—C18—C192.7 (3)
N1—C2—C3—N455.6 (2)C16—C17—C18—C23−176.61 (18)
N4—C5—C6—N1−54.2 (2)C17—C18—C19—C20178.81 (18)
N4—C5—C6—C7−175.72 (18)C23—C18—C19—C20−1.9 (3)
O9—C10—C11—C12−74.83 (17)C17—C18—C23—C111.10 (18)
O9—C10—C11—C2344.87 (17)C17—C18—C23—C22−178.39 (16)
C10—C11—C12—C13−56.5 (2)C19—C18—C23—C11−178.32 (16)
C10—C11—C12—C17128.77 (15)C19—C18—C23—C222.2 (3)
C23—C11—C12—C13177.33 (17)C18—C19—C20—C210.2 (3)
C23—C11—C12—C172.55 (16)C19—C20—C21—C221.3 (3)
C10—C11—C23—C18−130.26 (14)C20—C21—C22—C23−1.0 (3)
C10—C11—C23—C2249.2 (2)C21—C22—C23—C11179.91 (18)
C12—C11—C23—C18−2.18 (16)C21—C22—C23—C18−0.7 (3)
C12—C11—C23—C22177.26 (17)
D—H···AD—HH···AD···AD—H···A
N1—H1A···Cl1v1.062.083.117 (2)165.
N1—H1B···Cl1vi0.882.263.135 (2)171.
C2—H2B···O8vii0.962.413.316 (2)157.
C3—H3B···O80.962.382.778 (3)104.
C5—H5A···O90.962.232.665 (2)106.
C21—H21···O8xi0.982.543.469 (2)158.
C22—H22···Cl10.962.723.622 (2)157.
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1A⋯Cl1i1.062.083.117 (2)165
N1—H1B⋯Cl1ii0.882.263.135 (2)171
C2—H2B⋯O8iii0.962.413.316 (2)157
C21—H21⋯O8iv0.982.543.469 (2)158
C22—H22⋯Cl10.962.723.622 (2)157

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) .

  4 in total

1.  4-(Pyrazol-4-yl)-pyrimidines as selective inhibitors of cyclin-dependent kinase 4/6.

Authors:  Young Shin Cho; Maria Borland; Christopher Brain; Christine H-T Chen; Hong Cheng; Rajiv Chopra; Kristy Chung; James Groarke; Guo He; Ying Hou; Sunkyu Kim; Steven Kovats; Yipin Lu; Marc O'Reilly; Junqing Shen; Troy Smith; Gary Trakshel; Markus Vögtle; Mei Xu; Ming Xu; Moo Je Sung
Journal:  J Med Chem       Date:  2010-11-01       Impact factor: 7.446

2.  A short history of SHELX.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr A       Date:  2007-12-21       Impact factor: 2.290

3.  Inhibitors of human immunodeficiency virus type 1 (HIV-1) attachment. 5. An evolution from indole to azaindoles leading to the discovery of 1-(4-benzoylpiperazin-1-yl)-2-(4,7-dimethoxy-1H-pyrrolo[2,3-c]pyridin-3-yl)ethane-1,2-dione (BMS-488043), a drug candidate that demonstrates antiviral activity in HIV-1-infected subjects.

Authors:  Tao Wang; Zhiwei Yin; Zhongxing Zhang; John A Bender; Zhong Yang; Graham Johnson; Zheng Yang; Lisa M Zadjura; Celia J D'Arienzo; Dawn DiGiugno Parker; Christophe Gesenberg; Gregory A Yamanaka; Yi-Fei Gong; Hsu-Tso Ho; Hua Fang; Nannan Zhou; Brian V McAuliffe; Betsy J Eggers; Li Fan; Beata Nowicka-Sans; Ira B Dicker; Qi Gao; Richard J Colonno; Pin-Fang Lin; Nicholas A Meanwell; John F Kadow
Journal:  J Med Chem       Date:  2009-12-10       Impact factor: 7.446

4.  Structure validation in chemical crystallography.

Authors:  Anthony L Spek
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  4 in total

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