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Simplified models for the crystal lattice of the sesquihydrate form of the hemi-sulfate salt of (5S,6S,9R)-5-amino-6-(2,3-difluorophenyl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridin-9-yl 4-(2-oxo-2,3-dihydro-1H-imidazol[4,5b]pyridin-1-yl)-1-piperidine carboxylate (BMS-927711, C28H29F2N6O3+) are used to calculate diffuse diffraction features in order to develop a mechanistic understanding of the dehydration process with respect to disruption of the lattice, since a Bragg model cannot be established. The model demonstrates that what we observe when the water leaves the crystal is partial transformation from the parent form to a child form (a new form, less hydrated and structurally related to the parent). Yet this `dried' structure is not a pure phase. It consists of semi-random layers of both child, parent and an interfacial layer which has a modulated structure that represents a transitory phase. Understanding the fact that a single `dried' crystal can have the disordered layer structure described as well as understanding mechanistic relationships between the phases involved can have implications in understanding the effect of common large scale bulk drying procedures. During the development of BMS-927711, difficulties did arise during characterization of the dried bulk when using only routine solid-state analysis. The material is now better understood from this diffraction study. The diffraction experiments also reveal intermodulation satellites, which upon interpretation yield even more structural information about the crystal transformation. The model suggests the mechanism of transformation is laminar in which layers of the crystal are driven to approach a stable B-centered supercell phase of lower water content.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S2052520614005125/wf5109sup1.cif
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2052520614005125/wf5109Isup2.hkl
Contains datablock I

pdf

Portable Document Format (PDF) file https://doi.org/10.1107/S2052520614005125/wf5109sup3.pdf
Figures showing reciprocal space sections, and observed and calculated precession images

CCDC reference: 990303

Computing details top

Data collection: Bruker APEX2; cell refinement: Bruker SAINT; data reduction: Bruker SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Bruker SHELXTL; software used to prepare material for publication: Bruker SHELXTL.

BMS-927711–0.5H2SO4 H1.5–1 sesquihydrate CGRP top
Crystal data top
C28H29F2N6O3+·0.5(O4S2)·1.5(H2O)F(000) = 1280
Mr = 610.63Dx = 1.423 Mg m3
Orthorhombic, P21212Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P_2_2abCell parameters from 7294 reflections
a = 10.9169 (9) Åθ = 2.7–54.0°
b = 33.039 (3) ŵ = 1.27 mm1
c = 7.9038 (6) ÅT = 296 K
V = 2850.8 (4) Å3Prism, colorless
Z = 40.26 × 0.22 × 0.18 mm
Data collection top
Bruker APEX-II CCD
diffractometer
3509 independent reflections
Radiation source: fine-focus sealed tube3235 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.035
φ and ω scansθmax = 55.1°, θmin = 2.7°
Absorption correction: multi-scan
SADABS (Sheldrick, 1996)
h = 1111
Tmin = 0.755, Tmax = 0.796k = 3534
18471 measured reflectionsl = 88
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.038H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.100 w = 1/[σ2(Fo2) + (0.056P)2 + 1.0338P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
3509 reflectionsΔρmax = 0.39 e Å3
399 parametersΔρmin = 0.18 e Å3
5 restraintsAbsolute structure: Flack H D (1983), Acta Cryst. A39, 876-881
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.01 (3)
Special details top

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
xyzUiso*/UeqOcc. (<1)
C10.7702 (3)0.86785 (9)0.5047 (4)0.0448 (8)
C20.7665 (3)0.83757 (9)0.6299 (4)0.0433 (8)
C30.9272 (3)0.87905 (9)0.6797 (4)0.0435 (8)
C40.6025 (4)0.84318 (13)0.3770 (5)0.0699 (11)
H40.54480.84440.29060.084*
C50.5920 (4)0.81282 (13)0.4927 (5)0.0684 (11)
H50.52740.79460.48400.082*
C60.6764 (3)0.80866 (11)0.6238 (5)0.0577 (9)
H60.67200.78770.70210.069*
C70.9084 (3)0.82233 (9)0.8839 (4)0.0456 (8)
H70.97270.83890.93550.055*
C80.9695 (3)0.78267 (10)0.8327 (5)0.0537 (9)
H8A0.90990.76500.77910.064*
H8B1.03450.78800.75200.064*
C91.0218 (3)0.76215 (11)0.9881 (5)0.0632 (10)
H9A1.05430.73590.95690.076*
H9B1.08870.77831.03270.076*
C100.8686 (4)0.79452 (10)1.1700 (4)0.0581 (9)
H10A0.92810.81211.22380.070*
H10B0.80470.78861.25170.070*
C110.8134 (3)0.81586 (10)1.0190 (4)0.0527 (9)
H11A0.74670.79980.97380.063*
H11B0.78030.84181.05410.063*
C120.8697 (3)0.72181 (9)1.1470 (4)0.0446 (8)
C130.7480 (3)0.68155 (12)0.6484 (5)0.0633 (10)
H130.75670.70290.57270.076*
C140.6737 (4)0.64982 (12)0.6034 (5)0.0665 (10)
H140.63530.64930.49840.080*
C150.6572 (3)0.61860 (11)0.7183 (5)0.0560 (9)
H150.60640.59690.69160.067*
C160.7163 (3)0.61982 (9)0.8726 (4)0.0450 (8)
C170.7940 (3)0.65271 (9)0.9039 (4)0.0465 (8)
C180.7080 (3)0.58701 (9)1.0058 (4)0.0466 (8)
H180.70400.60021.11670.056*
C190.8201 (3)0.55907 (9)1.0055 (4)0.0482 (8)
H190.80750.54060.91020.058*
C200.9403 (3)0.58149 (10)0.9660 (5)0.0539 (9)
H20A1.00710.56260.98310.065*
H20B0.93950.58840.84670.065*
C210.9708 (3)0.62003 (10)1.0646 (5)0.0544 (9)
H21A1.04500.63161.01750.065*
H21B0.98820.61261.18090.065*
C220.8709 (3)0.65265 (9)1.0646 (4)0.0467 (8)
H220.81730.64861.16260.056*
C230.8230 (3)0.53227 (10)1.1619 (4)0.0488 (8)
C240.8222 (3)0.49037 (11)1.1444 (5)0.0642 (10)
H240.81910.47921.03440.077*
C250.8278 (3)0.46539 (15)1.2797 (7)0.0846 (14)
H250.82430.43811.26220.101*
C260.8326 (4)0.47904 (17)1.4381 (7)0.0884 (14)
H260.83030.46131.52960.106*
C270.8409 (4)0.51975 (18)1.4617 (6)0.0867 (14)
C280.8331 (4)0.54614 (13)1.3244 (5)0.0716 (12)
N10.8644 (2)0.84509 (7)0.7370 (3)0.0446 (6)
N20.8677 (2)0.89196 (7)0.5375 (3)0.0476 (7)
H20.88910.91250.47740.057*
N30.6912 (3)0.87166 (9)0.3793 (4)0.0600 (8)
N40.9279 (3)0.75706 (8)1.1190 (4)0.0532 (7)
N50.8091 (3)0.68348 (8)0.7965 (4)0.0543 (7)
N60.5959 (2)0.56172 (8)0.9862 (4)0.0534 (7)
H6A0.60540.54490.89920.080*
H6B0.53160.57770.96750.080*
H6C0.58360.54751.08030.080*
O11.0190 (2)0.89331 (7)0.7438 (3)0.0618 (6)
O20.7746 (2)0.71789 (7)1.2241 (3)0.0616 (6)
O30.9356 (2)0.69038 (6)1.0833 (3)0.0509 (6)
O40.3908 (2)0.49846 (8)0.7592 (3)0.0659 (7)
O50.4930 (3)0.53644 (7)0.5467 (3)0.0749 (8)
S10.50000.50000.64941 (14)0.0455 (3)
O1S0.50000.50000.2134 (5)0.0820 (11)
H1SA0.48640.52190.26590.123*
O2S0.3401 (3)0.57842 (8)0.8737 (4)0.0800 (8)
H2SA0.33800.55330.85250.120*
H2SB0.29050.59090.81070.120*
F10.8437 (3)0.58440 (8)1.3581 (3)0.0868 (11)0.817 (5)
F20.8604 (4)0.53426 (12)1.6124 (4)0.1079 (13)0.817 (5)
F1A0.8206 (8)0.4781 (5)0.9853 (10)0.114 (6)*0.183 (5)
F2A0.8316 (9)0.4256 (2)1.266 (3)0.159 (8)*0.183 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.045 (2)0.0464 (18)0.0433 (19)0.0033 (15)0.0001 (18)0.0055 (15)
C20.0402 (19)0.0449 (17)0.0449 (18)0.0008 (15)0.0003 (17)0.0031 (16)
C30.046 (2)0.0419 (18)0.042 (2)0.0034 (16)0.0003 (17)0.0005 (15)
C40.054 (2)0.093 (3)0.063 (3)0.010 (2)0.020 (2)0.004 (2)
C50.052 (2)0.083 (3)0.070 (3)0.024 (2)0.008 (2)0.003 (2)
C60.056 (2)0.064 (2)0.053 (2)0.0154 (18)0.005 (2)0.0046 (17)
C70.0461 (19)0.0446 (17)0.046 (2)0.0073 (14)0.0118 (17)0.0078 (15)
C80.050 (2)0.054 (2)0.057 (2)0.0021 (16)0.0121 (18)0.0117 (17)
C90.048 (2)0.057 (2)0.084 (3)0.0025 (17)0.005 (2)0.020 (2)
C100.075 (2)0.0475 (19)0.052 (2)0.0057 (19)0.004 (2)0.0002 (16)
C110.064 (2)0.0449 (18)0.049 (2)0.0024 (16)0.0021 (19)0.0034 (15)
C120.046 (2)0.051 (2)0.0369 (18)0.0023 (17)0.0115 (18)0.0056 (16)
C130.060 (2)0.067 (2)0.062 (3)0.0022 (19)0.001 (2)0.010 (2)
C140.063 (2)0.076 (3)0.060 (2)0.003 (2)0.013 (2)0.001 (2)
C150.049 (2)0.058 (2)0.061 (2)0.0013 (17)0.0095 (19)0.0097 (19)
C160.0386 (17)0.0463 (17)0.050 (2)0.0023 (15)0.0017 (17)0.0073 (16)
C170.0385 (18)0.0491 (19)0.052 (2)0.0004 (15)0.0042 (17)0.0041 (16)
C180.0412 (18)0.0478 (17)0.051 (2)0.0102 (15)0.0080 (17)0.0130 (15)
C190.051 (2)0.0475 (18)0.0460 (19)0.0009 (15)0.0094 (17)0.0116 (15)
C200.0462 (19)0.057 (2)0.059 (2)0.0048 (16)0.0067 (18)0.0009 (18)
C210.0451 (19)0.0560 (19)0.062 (2)0.0024 (16)0.0018 (17)0.0081 (17)
C220.0437 (18)0.0449 (18)0.052 (2)0.0085 (15)0.0006 (17)0.0011 (15)
C230.0395 (18)0.058 (2)0.049 (2)0.0014 (15)0.0070 (17)0.0001 (17)
C240.060 (2)0.064 (2)0.068 (2)0.0067 (18)0.006 (2)0.018 (2)
C250.079 (3)0.081 (3)0.094 (4)0.014 (2)0.035 (3)0.014 (3)
C260.079 (3)0.098 (4)0.089 (4)0.002 (3)0.014 (3)0.031 (3)
C270.084 (3)0.133 (4)0.044 (3)0.037 (3)0.004 (2)0.002 (3)
C280.085 (3)0.081 (3)0.049 (2)0.028 (2)0.014 (2)0.009 (2)
N10.0444 (15)0.0418 (14)0.0474 (16)0.0098 (12)0.0088 (15)0.0067 (12)
N20.0526 (16)0.0432 (14)0.0469 (16)0.0066 (13)0.0029 (15)0.0051 (12)
N30.0532 (18)0.074 (2)0.0528 (18)0.0002 (16)0.0116 (17)0.0042 (15)
N40.0537 (16)0.0484 (16)0.0575 (18)0.0059 (13)0.0013 (16)0.0124 (14)
N50.0511 (17)0.0587 (17)0.0532 (18)0.0016 (14)0.0042 (15)0.0046 (14)
N60.0520 (17)0.0488 (15)0.0594 (18)0.0053 (13)0.0091 (15)0.0119 (14)
O10.0610 (16)0.0610 (14)0.0633 (15)0.0266 (12)0.0119 (15)0.0071 (12)
O20.0555 (15)0.0637 (15)0.0657 (16)0.0076 (12)0.0118 (14)0.0056 (13)
O30.0451 (12)0.0477 (12)0.0600 (15)0.0097 (11)0.0033 (11)0.0008 (11)
O40.0544 (14)0.0680 (15)0.0752 (16)0.0066 (12)0.0120 (13)0.0230 (15)
O50.102 (2)0.0499 (13)0.0729 (17)0.0152 (14)0.0111 (18)0.0209 (12)
S10.0573 (7)0.0355 (6)0.0436 (6)0.0002 (5)0.0000.000
O1S0.106 (3)0.079 (2)0.061 (2)0.004 (2)0.0000.000
O2S0.0904 (19)0.0647 (15)0.0848 (19)0.0085 (14)0.0066 (17)0.0017 (14)
F10.129 (3)0.0764 (19)0.0553 (16)0.0257 (17)0.0149 (18)0.0219 (14)
F20.131 (3)0.145 (3)0.0477 (18)0.045 (2)0.0083 (19)0.0040 (18)
Geometric parameters (Å, º) top
C1—N31.320 (4)C16—C181.514 (5)
C1—N21.355 (4)C17—N51.335 (4)
C1—C21.408 (5)C17—C221.523 (5)
C2—C61.372 (5)C18—N61.491 (4)
C2—N11.386 (4)C18—C191.533 (5)
C3—O11.217 (4)C18—H180.9800
C3—N21.366 (4)C19—C231.521 (5)
C3—N11.391 (4)C19—C201.539 (5)
C4—N31.350 (5)C19—H190.9800
C4—C51.362 (6)C20—C211.530 (5)
C4—H40.9300C20—H20A0.9700
C5—C61.394 (5)C20—H20B0.9700
C5—H50.9300C21—C221.533 (4)
C6—H60.9300C21—H21A0.9700
C7—N11.464 (4)C21—H21B0.9700
C7—C111.504 (5)C22—O31.440 (4)
C7—C81.525 (5)C22—H220.9800
C7—H70.9800C23—C281.368 (5)
C8—C91.515 (5)C23—C241.391 (5)
C8—H8A0.9700C24—C251.352 (6)
C8—H8B0.9700C24—H240.9451
C9—N41.466 (5)C25—C261.332 (7)
C9—H9A0.9700C25—H250.9133
C9—H9B0.9700C26—C271.361 (7)
C10—N41.454 (4)C26—H260.9300
C10—C111.511 (5)C27—F21.302 (5)
C10—H10A0.9700C27—C281.395 (6)
C10—H10B0.9700C28—F11.297 (5)
C11—H11A0.9700N2—H20.8600
C11—H11B0.9700N6—H6A0.8900
C12—O21.211 (4)N6—H6B0.8900
C12—N41.345 (4)N6—H6C0.8900
C12—O31.360 (4)O4—S11.476 (2)
C13—N51.349 (5)O5—S11.454 (2)
C13—C141.372 (5)S1—O5i1.454 (2)
C13—H130.9300S1—O4i1.476 (2)
C14—C151.386 (5)O1S—H1SA0.8461
C14—H140.9300O2S—H2SA0.8481
C15—C161.380 (5)O2S—H2SB0.8439
C15—H150.9300F1A—H240.3905
C16—C171.401 (4)F2A—H250.4225
N3—C1—N2127.0 (3)C16—C18—H18107.8
N3—C1—C2125.2 (3)C19—C18—H18107.8
N2—C1—C2107.8 (3)C23—C19—C18111.5 (3)
C6—C2—N1134.4 (3)C23—C19—C20115.3 (3)
C6—C2—C1119.4 (3)C18—C19—C20113.0 (3)
N1—C2—C1106.2 (3)C23—C19—H19105.3
O1—C3—N2127.8 (3)C18—C19—H19105.3
O1—C3—N1125.6 (3)C20—C19—H19105.3
N2—C3—N1106.6 (3)C21—C20—C19118.9 (3)
N3—C4—C5124.4 (4)C21—C20—H20A107.6
N3—C4—H4117.8C19—C20—H20A107.6
C5—C4—H4117.8C21—C20—H20B107.6
C4—C5—C6121.1 (3)C19—C20—H20B107.6
C4—C5—H5119.5H20A—C20—H20B107.0
C6—C5—H5119.5C20—C21—C22115.5 (3)
C2—C6—C5115.6 (3)C20—C21—H21A108.4
C2—C6—H6122.2C22—C21—H21A108.4
C5—C6—H6122.2C20—C21—H21B108.4
N1—C7—C11114.2 (3)C22—C21—H21B108.4
N1—C7—C8112.0 (3)H21A—C21—H21B107.5
C11—C7—C8111.6 (3)O3—C22—C17110.8 (3)
N1—C7—H7106.1O3—C22—C21105.0 (2)
C11—C7—H7106.1C17—C22—C21113.1 (3)
C8—C7—H7106.1O3—C22—H22109.3
C9—C8—C7109.5 (3)C17—C22—H22109.3
C9—C8—H8A109.8C21—C22—H22109.3
C7—C8—H8A109.8C28—C23—C24115.3 (4)
C9—C8—H8B109.8C28—C23—C19124.7 (3)
C7—C8—H8B109.8C24—C23—C19119.9 (3)
H8A—C8—H8B108.2C25—C24—C23121.9 (4)
N4—C9—C8111.1 (3)C25—C24—H24119.4
N4—C9—H9A109.4C23—C24—H24118.7
C8—C9—H9A109.4C26—C25—C24122.6 (5)
N4—C9—H9B109.4C26—C25—H25118.6
C8—C9—H9B109.4C24—C25—H25118.8
H9A—C9—H9B108.0C25—C26—C27117.8 (5)
N4—C10—C11110.8 (3)C25—C26—H26121.1
N4—C10—H10A109.5C27—C26—H26121.1
C11—C10—H10A109.5F2—C27—C26120.0 (5)
N4—C10—H10B109.5F2—C27—C28119.5 (5)
C11—C10—H10B109.5C26—C27—C28120.5 (5)
H10A—C10—H10B108.1F1—C28—C23121.8 (4)
C7—C11—C10110.6 (3)F1—C28—C27116.3 (4)
C7—C11—H11A109.5C23—C28—C27121.7 (4)
C10—C11—H11A109.5C2—N1—C3109.0 (3)
C7—C11—H11B109.5C2—N1—C7130.2 (2)
C10—C11—H11B109.5C3—N1—C7120.7 (3)
H11A—C11—H11B108.1C1—N2—C3110.3 (3)
O2—C12—N4125.5 (3)C1—N2—H2124.8
O2—C12—O3124.0 (3)C3—N2—H2124.8
N4—C12—O3110.5 (3)C1—N3—C4114.3 (3)
N5—C13—C14123.6 (4)C12—N4—C10118.7 (3)
N5—C13—H13118.2C12—N4—C9123.1 (3)
C14—C13—H13118.2C10—N4—C9114.2 (3)
C13—C14—C15118.4 (4)C17—N5—C13117.1 (3)
C13—C14—H14120.8C18—N6—H6A109.5
C15—C14—H14120.8C18—N6—H6B109.5
C16—C15—C14119.7 (3)H6A—N6—H6B109.5
C16—C15—H15120.1C18—N6—H6C109.5
C14—C15—H15120.1H6A—N6—H6C109.5
C15—C16—C17117.5 (3)H6B—N6—H6C109.5
C15—C16—C18124.5 (3)C12—O3—C22116.0 (2)
C17—C16—C18117.9 (3)O5—S1—O5i112.1 (2)
N5—C17—C16123.6 (3)O5—S1—O4i110.02 (16)
N5—C17—C22117.6 (3)O5i—S1—O4i108.34 (15)
C16—C17—C22118.7 (3)O5—S1—O4108.34 (15)
N6—C18—C16112.2 (3)O5i—S1—O4110.02 (16)
N6—C18—C19108.5 (2)O4i—S1—O4107.9 (2)
C16—C18—C19112.5 (3)H2SA—O2S—H2SB110.2
N6—C18—H18107.8
Symmetry code: (i) x+1, y+1, z.
 

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