Literature DB >> 22412567

Clarithromycin monohydrate: a synchrotron X-ray powder study.

Shuji Noguchi, Sadahiro Fujiki, Yasunori Iwao, Keiko Miura, Shigeru Itai.   

Abstract

In the crystal structure of the title compound, clarithromycin (CAM) monohydrate, C(38)H(69)NO(13)·H(2)O, the water mol-ecule behaves as a proton donor and is hydrogen bonded to the hy-droxy O atom of the CAM cladinose ring. The hy-droxy O atom also behaves as a proton donor, forming an inter-molecular hydrogen bond with one of the hy-droxy groups of the 14-membered aglycone ring. The CAM mol-ecules are linked through these hydrogen bonds into chains running parallel to the c axis.

Entities:  

Year:  2012        PMID: 22412567      PMCID: PMC3295456          DOI: 10.1107/S1600536812005090

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


Related literature

For background to the title compound, see Avrutov et al. (2003 ▶); Noguchi, Fujiki et al. (2012 ▶). For information relating to the pharmaceutical properties of CAM, see: Yajima et al. (1999 ▶, 2002 ▶); Fujiki et al. (2011 ▶); Liu et al. (1999 ▶). For related structures, see: Noguchi, Miura et al. (2012 ▶; form I, anhydrate); Jin et al. (2011 ▶; form 0, ethanol solvate); Stephenson et al. (1997 ▶; form II, anhydrate); Liang & Yao (2008 ▶; form III, acetonitrile solvate); Parvez et al. (2000 ▶; hydro­chloride salt); Iwasaki et al. (1993 ▶; methanol solvate).

Experimental

Crystal data

C38H69NO13·H2O M = 765.97 Orthorhombic, a = 15.6999 (2) Å b = 18.8817 (2) Å c = 15.0267 (2) Å V = 4454.53 (9) Å3 Z = 4 Synchrotron radiation, λ = 1.3000 Å μ = 0.41 mm−1 T = 298 K cylinder, 3.0 × 0.3 mm

Data collection

BL-19B2 Debye–Scherrer camera diffractometer Specimen mounting: capilary Data collection mode: transmission Scan method: Stationary detector 2θfixed = 65

Refinement

R p = 0.038 R wp = 0.052 R exp = 0.016 R Bragg = 0.059 R(F) = 0.076 R(F 2) = 0.07617 χ2 = 11.020 6201 data points 188 parameters 96 restraints H-atom parameters not refined Data collection: local software (Osaka et al., 2010 ▶; Takata et al., 2002 ▶); cell refinement: EXPO2009 (Altomare et al., 2009 ▶) and RIETAN-FP (Izumi & Momma, 2007 ▶); data reduction: local software (Takata et al., 2002 ▶); program(s) used to solve structure: CCP4 (Collaborative Computational Project, Number 4, 1994 ▶); program(s) used to refine structure: CCP4, RIETAN-FP and Jmol (Hanson, 2010 ▶); molecular graphics: CCP4MG (McNicholas et al., 2011 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶). Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812005090/hb6588sup1.cif Rietveld powder data: contains datablock(s) I. DOI: 10.1107/S1600536812005090/hb6588Isup2.rtv Supplementary material file. DOI: 10.1107/S1600536812005090/hb6588Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C38H69NO13·H2OF(000) = 1672.00
Mr = 765.97Dx = 1.142 Mg m3
Orthorhombic, P212121Synchrotron radiation, λ = 1.3000 Å
Hall symbol: P 2ac 2abµ = 0.41 mm1
a = 15.6999 (2) ÅT = 298 K
b = 18.8817 (2) ÅParticle morphology: powder
c = 15.0267 (2) Åwhite
V = 4454.53 (9) Å3cylinder, 3.0 × 0.3 mm
Z = 4Specimen preparation: Prepared at 298 K and 101 kPa
BL-19B2 Debye–Scherrer camera diffractometerData collection mode: transmission
Radiation source: synchrotron, SPring-8 BL19B2Scan method: Stationary detector
Si(111) monochromatorfixed = 65
Specimen mounting: capilary
Least-squares matrix: selected elements onlyProfile function: split pseudo-Voigt function
Rp = 0.038188 parameters
Rwp = 0.05296 restraints
Rexp = 0.0160 constraints
RBragg = 0.059H-atom parameters not refined
R(F) = 0.076Weighting scheme based on measured s.u.'s 1/[Yi]
R(F2) = 0.07617(Δ/σ)max = 0.011
χ2 = 11.020Background function: Legendre polynomials
6201 data points
xyzUiso*/Ueq
O10.024 (1)0.1102 (8)0.205 (1)0.066 (5)*
C10.154 (2)−0.074 (2)0.101 (2)0.066 (5)*
O20.108 (2)0.1127 (9)0.327 (1)0.066 (5)*
C20.217 (3)−0.007 (2)−0.026 (1)0.066 (5)*
O30.256 (1)0.079 (1)0.220 (2)0.066 (5)*
C30.156 (1)0.0568 (7)0.095 (1)0.066 (5)*
O40.051 (1)0.356 (1)0.609 (1)0.066 (5)*
C40.168 (1)0.065 (1)0.197 (1)0.066 (5)*
O50.166 (1)0.286 (1)0.638 (1)0.066 (5)*
C50.107 (1)0.119 (1)0.236 (1)0.066 (5)*
O60.089 (1)0.239 (1)0.8636 (9)0.066 (5)*
C60.0191 (8)0.1221 (7)0.111 (1)0.066 (5)*
O7−0.0338 (9)0.2408 (9)0.740 (2)0.066 (5)*
C70.064 (1)0.062 (1)0.068 (1)0.066 (5)*
O8−0.1207 (9)0.122 (1)0.670 (1)0.066 (5)*
C8−0.073 (1)0.117 (1)0.092 (2)0.066 (5)*
O9−0.032 (2)0.210 (1)0.484 (2)0.066 (5)*
C90.079 (1)0.176 (1)0.374 (1)0.066 (5)*
C100.150 (1)0.221 (1)0.422 (1)0.066 (5)*
C110.236 (1)0.213 (1)0.372 (2)0.066 (5)*
C120.121 (1)0.297 (1)0.419 (1)0.066 (5)*
C130.165 (1)0.341 (1)0.495 (1)0.066 (5)*
C140.170 (2)0.420 (1)0.473 (2)0.066 (5)*
C150.118 (1)0.329 (1)0.586 (1)0.066 (5)*
C160.1654 (9)0.2915 (7)0.737 (1)0.066 (5)*
C170.133 (1)0.3633 (7)0.763 (1)0.066 (5)*
C180.207 (2)0.411 (1)0.784 (3)0.066 (5)*
C190.1174 (8)0.2269 (6)0.7706 (8)0.066 (5)*
C200.179 (1)0.1663 (7)0.777 (2)0.066 (5)*
C210.0398 (9)0.205 (1)0.709 (1)0.066 (5)*
C220.0214 (9)0.1267 (8)0.708 (2)0.066 (5)*
C23−0.005 (2)0.095 (2)0.797 (2)0.066 (5)*
C24−0.0497 (8)0.109 (1)0.645 (1)0.066 (5)*
C25−0.028 (1)0.0617 (8)0.564 (1)0.066 (5)*
C260.012 (2)−0.008 (1)0.599 (2)0.066 (5)*
C270.036 (1)0.095 (1)0.502 (2)0.066 (5)*
C280.003 (2)0.1505 (9)0.434 (1)0.066 (5)*
C29−0.060 (1)0.113 (2)0.371 (2)0.066 (5)*
N10.198 (1)−0.0086 (9)0.071 (1)0.066 (5)*
C30−0.108 (2)0.245 (2)0.457 (3)0.066 (5)*
C310.096 (1)0.3798 (7)0.282 (1)0.066 (5)*
C320.147 (2)0.4097 (8)0.204 (2)0.066 (5)*
C330.144 (2)0.3696 (9)0.113 (2)0.066 (5)*
C340.181 (3)0.418 (2)0.044 (2)0.066 (5)*
C350.259 (2)0.288 (1)0.164 (2)0.066 (5)*
C360.050 (1)0.355 (2)0.089 (2)0.066 (5)*
C370.0039 (9)0.319 (2)0.166 (2)0.066 (5)*
C38−0.088 (1)0.309 (2)0.147 (2)0.066 (5)*
O100.148 (1)0.326 (1)0.322 (1)0.066 (5)*
O110.189 (1)0.301 (1)0.109 (2)0.066 (5)*
O120.040 (2)0.310 (1)0.013 (2)0.066 (5)*
O130.013 (1)0.357 (1)0.251 (1)0.066 (5)*
O14−0.108 (2)0.328 (1)−0.069 (2)0.066 (5)*
H10.18752−0.114450.084650.066*
H20.14803−0.07240.164570.066*
H30.09936−0.076530.073540.066*
H40.16522−0.00535−0.05870.066*
H50.251910.03289−0.039530.066*
H60.24771−0.05005−0.041390.066*
H70.181590.095220.062360.066*
H80.153380.020440.22340.066*
H90.125610.164820.217950.066*
H100.043570.166090.092040.066*
H110.061590.069380.004060.066*
H120.035730.019070.082520.066*
H13−0.102420.154810.122780.066*
H14−0.082170.121970.029350.066*
H15−0.09440.072450.112070.066*
H160.059240.211740.333470.066*
H170.158660.204170.481940.066*
H180.225160.214230.309050.066*
H190.271910.252470.387710.066*
H200.262420.169850.388110.066*
H210.06070.302250.428370.066*
H220.221660.323060.501040.066*
H230.113380.439680.468830.066*
H240.201020.44450.518480.066*
H250.198350.426290.416720.066*
H260.220070.289540.764840.066*
H270.100260.383180.715590.066*
H280.098150.359080.815420.066*
H290.239050.419510.730170.066*
H300.185420.456210.80510.066*
H310.242740.390060.828330.066*
H320.149170.124510.795050.066*
H330.205860.159150.721050.066*
H340.221660.177690.82140.066*
H350.055220.218680.649640.066*
H360.075030.106240.69070.066*
H37−0.063120.107940.809890.066*
H380.000250.04470.795650.066*
H390.031080.113870.84370.066*
H40−0.080130.053860.532190.066*
H41−0.02796−0.032310.63740.066*
H420.02733−0.038130.550890.066*
H430.062420.002860.633870.066*
H440.078150.1180.537980.066*
H450.061970.057360.46870.066*
H46−0.085480.146650.331880.066*
H47−0.030380.077540.336670.066*
H48−0.103690.090030.405680.066*
H49−0.146750.210360.433560.066*
H50−0.13280.267880.50730.066*
H51−0.094140.278840.412130.066*
H520.081970.413890.327420.066*
H530.125290.4570.193850.066*
H540.204520.412090.223140.066*
H550.241590.424590.057030.066*
H560.176310.39594−0.013180.066*
H570.153250.462670.044790.066*
H580.249940.306590.222270.066*
H590.270450.238380.16690.066*
H600.308030.311410.138020.066*
H610.026180.401020.074670.066*
H620.030890.273170.171690.066*
H63−0.095860.271160.104680.066*
H64−0.118280.297640.200710.066*
H65−0.111270.351980.122180.066*
H660.287010.067790.178280.066*
H670.045990.264220.865130.066*
H68−0.076620.216610.731700.066*
H690.072040.275400.017970.066*
H70−0.058540.31967−0.032280.066*
H71−0.091980.31147−0.126510.066*
O1—C51.39 (2)C5—H90.96
O1—C61.43 (2)O6—H670.82
C1—N11.49 (4)C6—H100.96
O2—C51.37 (2)O7—H680.82
O2—C91.46 (3)C7—H120.96
C2—N11.49 (2)C7—H110.96
O3—C41.45 (2)C8—H140.96
C3—N11.45 (2)C8—H130.96
C3—C71.50 (2)C8—H150.96
C3—C41.55 (2)C9—H160.96
O4—C151.22 (2)C10—H170.96
C4—C51.52 (2)C11—H200.96
O5—C151.36 (2)C11—H190.96
O5—C161.49 (2)C11—H180.96
O6—C191.485 (18)C12—H210.96
C6—C81.48 (2)C13—H220.96
C6—C71.48 (2)C14—H250.96
O7—C211.42 (2)C14—H240.96
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O9—C301.42 (4)C16—H260.96
O9—C281.46 (3)C17—H270.96
C9—C281.57 (3)C17—H280.96
C9—C101.58 (2)C18—H310.96
C10—C121.51 (3)C18—H300.96
C10—C111.55 (3)C18—H290.96
C12—C131.57 (2)C20—H330.96
C13—C141.53 (3)C20—H320.96
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C22—C231.52 (4)C26—H430.96
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C32—C331.56 (4)C30—H490.96
C33—O111.48 (3)C31—H520.96
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C35—O111.40 (4)C34—H570.96
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C5—O1—C6111.2 (13)H15—C8—C6109.3
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N1—C3—C4106.0 (13)H16—C9—C28109.9
C7—C3—C4112.1 (13)H17—C10—C12112.2
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C15—O5—C16122.0 (15)H20—C11—H19109.8
O2—C5—O1109.5 (18)H20—C11—H18111.0
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C8—C6—C7109.3 (14)H21—C12—C10112.4
C6—C7—C3112.9 (13)H21—C12—C13106.1
C30—O9—C28122 (3)H21—C12—O10110.8
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O2—C9—C10116.2 (17)H22—C13—C15108.2
C28—C9—C10116.1 (13)H22—C13—C12107.1
C12—C10—C11109.9 (14)H25—C14—H24110.0
C12—C10—C9106.6 (13)H25—C14—H23109.2
C11—C10—C9109.9 (14)H25—C14—C13109.6
C10—C12—C13110.4 (13)H24—C14—H23109.1
C10—C12—O10105.7 (13)H24—C14—C13109.5
C13—C12—O10111.2 (14)H23—C14—C13109.3
C14—C13—C15110.7 (17)H26—C16—O5115.5
C14—C13—C12112.4 (16)H26—C16—C17102.6
C15—C13—C12110.5 (13)H26—C16—C19105.4
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O4—C15—C13126.3 (16)H27—C17—C18109.7
O5—C15—C13109.1 (14)H27—C17—C16109.9
O5—C16—C17109.0 (13)H28—C17—C18108.6
O5—C16—C19106.2 (12)H28—C17—C16109.4
C17—C16—C19118.1 (12)H28—C17—H26109.2
C18—C17—C16109.5 (15)H31—C18—H30110.0
O6—C19—C20104.5 (15)H31—C18—H29109.6
O6—C19—C16109.8 (12)H31—C18—C17110.2
O6—C19—C21111.0 (11)H30—C18—H29108.5
C20—C19—C16108.3 (11)H30—C18—C17109.6
C20—C19—C21109.5 (13)H29—C18—C17108.9
C16—C19—C21113.4 (11)C16—C19—H67104.0
O7—C21—C22108.4 (13)H33—C20—H32110.3
O7—C21—C19108.1 (15)H33—C20—H34109.5
C22—C21—C19114.2 (14)H33—C20—C19109.5
C24—C22—C21111.6 (16)H32—C20—H34109.3
C24—C22—C23105.3 (16)H32—C20—C19109.4
C21—C22—C23115 (2)H34—C20—C19108.9
O8—C24—C22116.6 (16)H35—C21—O7113.0
O8—C24—C25124.6 (15)H35—C21—C22107.0
C22—C24—C25117.4 (13)H35—C21—C19106.5
C27—C25—C24113.1 (14)H35—C21—H68112.6
C27—C25—C26107.1 (16)H68—C21—H36113.9
C24—C25—C26108.2 (15)H36—C22—C24113.0
C25—C27—C28117.8 (16)H36—C22—C21103.2
O9—C28—C29115 (3)H36—C22—C23108.8
O9—C28—C27107.9 (17)H38—C23—H37110.1
O9—C28—C9110.2 (17)H38—C23—H39109.5
C29—C28—C27108.0 (19)H38—C23—C22109.8
C29—C28—C9106.0 (14)H37—C23—H39109.0
C27—C28—C9109 (2)H37—C23—C22109.3
C3—N1—C2108.6 (19)H39—C23—C22109.0
C3—N1—C1115.0 (18)H40—C25—C27108.6
C2—N1—C1114 (2)H40—C25—C24107.1
O10—C31—O13115.8 (14)H40—C25—C26112.5
O10—C31—C32106.6 (15)H42—C26—H43110.0
O13—C31—C32109.5 (16)H42—C26—H41109.9
C31—C32—C33118.4 (17)H42—C26—C25110.5
O11—C33—C34109 (3)H43—C26—H41108.1
O11—C33—C36107 (2)H43—C26—C25109.0
O11—C33—C32117 (2)H41—C26—C25109.3
C34—C33—C36109 (3)H44—C27—H45109.4
C34—C33—C32107.3 (19)H44—C27—C25107.1
C36—C33—C32109 (2)H44—C27—C28107.9
O12—C36—C37107 (3)H45—C27—C25106.6
O12—C36—C33113 (2)H45—C27—C28107.5
C37—C36—C33111 (2)H46—C29—H47110.0
O13—C37—C38109 (2)H46—C29—H48109.5
O13—C37—C36113 (3)H46—C29—C28109.3
C38—C37—C36112 (2)H47—C29—H48109.4
C31—O10—C12118.0 (13)H47—C29—C28109.6
C35—O11—C33120 (2)H48—C29—C28109.1
C31—O13—C37120.7 (14)H50—C30—H51110.6
H1—C1—H3110.1H50—C30—H49109.6
H1—C1—H2109.6H50—C30—O9109.3
H1—C1—N1109.5H51—C30—H49109.6
H3—C1—H2109.5H51—C30—O9108.9
H3—C1—N1109.3H49—C30—O9108.7
H2—C1—N1108.8H52—C31—O10107.6
H4—C2—H5110.2H52—C31—O13103.1
H4—C2—H6109.0H52—C31—C32114.4
H4—C2—N1110.3H54—C32—H53109.6
H5—C2—H6108.4H54—C32—C31106.8
H5—C2—N1110.0H54—C32—C33108.1
H6—C2—N1108.8H53—C32—C31106.4
H66—O3—C4110.0H53—C32—C33107.5
H66—O3—H8111.6H57—C34—H56111.2
H7—C3—N1108.6H57—C34—H55109.4
H7—C3—C7102.0H57—C34—C33110.3
H7—C3—C4112.3H56—C34—H55108.4
H8—C4—O3106.6H56—C34—C33109.0
H8—C4—C5106.2H55—C34—C33108.3
H8—C4—C3107.4H58—C35—H59110.7
H8—C4—H66108.7H58—C35—H60108.8
H9—C5—O2110.6H58—C35—O11110.8
H9—C5—O1106.9H59—C35—H60108.8
H9—C5—C4107.9H59—C35—O11110.0
O1—C5—H8101.8H60—C35—O11107.7
H67—O6—C19111.0H61—C36—O12108.6
H10—C6—O1114.5H61—C36—C37112.7
H10—C6—C8112.5H61—C36—C33105.1
H10—C6—C7109.4H62—C37—O13108.1
H68—O7—C21110.8H62—C37—C38109.4
H68—O7—H35110.4H62—C37—C36105.2
H12—C7—H11109.5H64—C38—H63109.3
H12—C7—C6109.0H64—C38—H65109.3
H12—C7—C3108.7H64—C38—C37110.3
H11—C7—C6108.5H63—C38—H65108.9
H11—C7—C3108.6H63—C38—C37109.7
C6—C7—H7103.0H65—C38—C37109.3
H14—C8—H13109.6C33—O11—H60111.0
H14—C8—H15109.5H69—O12—C36109.7
H14—C8—C6109.5C36—O12—H70110.3
H13—C8—H15109.5C31—O13—H62107.2
H13—C8—C6109.4H70—O14—H71104.5
D—H···AD—HH···AD···AD—H···A
O6—H67···O70.832.302.68 (3)108
O7—H68···O80.822.132.83 (3)143
O12—H69···O110.832.342.75 (4)111
O6—H67···O12i0.832.392.73 (3)105
O12—H69···O6ii0.832.432.73 (3)102
O14—H70···O120.971.702.65 (4)168
O14—H71···O7ii0.952.583.51 (4)166
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O6—H67⋯O70.832.302.68 (3)108
O7—H68⋯O80.822.132.83 (3)143
O12—H69⋯O110.832.342.75 (4)111
O6—H67⋯O12i0.832.392.73 (3)105
O12—H69⋯O6ii0.832.432.73 (3)102
O14—H70⋯O120.971.702.65 (4)168
O14—H71⋯O7ii0.952.583.51 (4)166

Symmetry codes: (i) ; (ii) .

  7 in total

1.  The CCP4 suite: programs for protein crystallography.

Authors: 
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1994-09-01

2.  Clarithromycin form I determined by synchrotron X-ray powder diffraction.

Authors:  Shuji Noguchi; Keiko Miura; Sadahiro Fujiki; Yasunori Iwao; Shigeru Itai
Journal:  Acta Crystallogr C       Date:  2012-01-06       Impact factor: 1.172

3.  Method of evaluation of the bitterness of clarithromycin dry syrup.

Authors:  Toshio Yajima; Yumiko Fukushima; Shigeru Itai; Yoshiaki Kawashima
Journal:  Chem Pharm Bull (Tokyo)       Date:  2002-02       Impact factor: 1.645

4.  Solid-state investigations of erythromycin A dihydrate: structure, NMR spectroscopy, and hygroscopicity.

Authors:  G A Stephenson; J G Stowell; P H Toma; R R Pfeiffer; S R Byrn
Journal:  J Pharm Sci       Date:  1997-11       Impact factor: 3.534

5.  Stabilization mechanism of clarithromycin tablets under gastric pH conditions.

Authors:  Sadahiro Fujiki; Yasunori Iwao; Mika Kobayashi; Atsuo Miyagishima; Shigeru Itai
Journal:  Chem Pharm Bull (Tokyo)       Date:  2011       Impact factor: 1.645

6.  Optimum spray congealing conditions for masking the bitter taste of clarithromycin in wax matrix.

Authors:  T Yajima; N Umeki; S Itai
Journal:  Chem Pharm Bull (Tokyo)       Date:  1999-02       Impact factor: 1.645

7.  Presenting your structures: the CCP4mg molecular-graphics software.

Authors:  S McNicholas; E Potterton; K S Wilson; M E M Noble
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18
  7 in total
  1 in total

1.  Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

Authors:  Jacco van de Streek; Marcus A Neumann
Journal:  Acta Crystallogr B Struct Sci Cryst Eng Mater       Date:  2014-12-01
  1 in total

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