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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296
Volume 66| Part 12| December 2010| Pages o585-o588
doi:10.1107/S0108270110044136

N-{N-[2-(3,5-Di­fluoro­phenyl)acetyl]-(S)-alanyl}-(S)-phenyl­glycine tert-butyl ester (DAPT): an inhibitor of γ-secretase, revealing fine electronic and hydrogen-bonding features

CROSSMARK_Color_square_no_text.svg
Andrzej Czerwinski,a Francisco Valenzuela,a Pavel Afonine,b Miroslawa Dauterc* and Zbigniew Dauterd

aPeptides International Inc., 11621 Electron Drive, Louisville, KY 40299, USA, bLawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720, USA, cBasic Research Program, SAIC–Frederick Inc., Synchrotron Radiation Research Section, MCL, NCI, Argonne National Laboratory, Biosciences Division, Building 202, Argonne, IL 60439, USA, and dSynchrotron Radiation Research Section, MCL, NCI, Argonne National Laboratory, Biosciences Division, Building 202, Argonne, IL 60439, USA
*Correspondence e-mail: dauter@anl.gov

(Received 16 September 2010; accepted 28 October 2010; online 6 November 2010)

The title compound, C23H26F2N2O4, is a dipeptidic inhibitor of γ-secretase, one of the enzymes involved in Alzheimer's dis­ease. The mol­ecule adopts a compact conformation, without intra­molecular hydrogen bonds. In the crystal structure, one of the amide N atoms forms the only inter­molecular N—H⋯O hydrogen bond; the second amide N atom does not form hydrogen bonds. High-resolution synchrotron diffraction data permitted the unequivocal location and refinement without restraints of all H atoms, and the identification of the characteristic shift of the amide H atom engaged in the hydrogen bond from its ideal position, resulting in a more linear hydrogen bond. Significant residual densities for bonding electrons were revealed after the usual SHELXL refinement, and modeling of these features as additional inter­atomic scatterers (IAS) using the program PHENIX led to a significant decrease in the R factor from 0.0411 to 0.0325 and diminished the r.m.s. deviation level of noise in the final difference Fourier map from 0.063 to 0.037 e Å−3.

Comment

Alzheimer's disease, a progressive neurodegenerative dis­order, is the most prominent contributor to senile dementia, a condition affecting millions of individuals worldwide. The disease is associated with the presence of extracellular plaques and intra­cellular neurofibrillary tangles in the brains of Alzheimer's sufferers (Goedert & Spillantini, 2006[Goedert, M. & Spillantini, M. G. (2006). Science, 314, 777-781.]). Amyloid-β plaque peptides are produced as a result of the sequential proteolytic cleavages of a protein precursor, involving β- and γ-secretase enzymes (Chapman et al., 2001[Chapman, P. F., Falinska, A. M., Knevett, S. G. & Ramsay, M. F. (2001). Trends Genet. 17, 254-261.]). A great amount of effort has been expended in exploring the use of the enzyme inhibitors and modulators aimed at preventing amyloid formation (Wolfe, 2008[Wolfe, M. S. (2008). Curr. Alzheimer Res. 5, 158-164.]). An approach based on targeting γ-secretase (Roberts, 2002[Roberts, S. B. (2002). Adv. Drug Deliv. Rev. 54, 1579-1588.]; Barten et al., 2006[Barten, D. M., Meredith, J. E., Zaczek, R., Houston, J. G. & Albright, C. F. (2006). Drugs R D, 7, 87-97.]; Tomita, 2008[Tomita, T. (2008). Naunyn-Schmiedeberg's Arch. Pharmacol. 377, 295-300.]) seems to be more promising (Wolfe, 2008[Wolfe, M. S. (2008). Curr. Alzheimer Res. 5, 158-164.]) than an approach that has been focused on β-secretase (Vassar, 2002[Vassar, R. (2002). Adv. Drug Deliv. Rev. 54, 1589-1602.]; Schmidt et al., 2006[Schmidt, B., Baumann, S., Braun, H. A. & Larbig, G. (2006). Curr. Top. Med. Chem. 6, 377-392.]). This research generated a number of potent and specific inhibitors, among them N-[N-(3,5-difluoro­phenyl­acetyl)-S-alanyl]-(S)-phenyl­glycine tert-butyl ester (DAPT) (Dovey et al., 2001[Dovey, H. F., et al. (2001). J. Neurochem. 76, 173-181.]). DAPT, (I)[link], has been shown to block amyloid-β production in human neuronal cultures, and its administration to transgenic mice resulted in the first successful reduction of amyloid level in vivo (Dovey et al., 2001[Dovey, H. F., et al. (2001). J. Neurochem. 76, 173-181.]; Lanz et al., 2003[Lanz, T. A., Himes, C. S., Pallante, G., Adams, L., Yamazaki, S., Amore, B. & Merchant, K. M. (2003). J. Pharmacol. Exp. Ther. 305, 864-871.]). Presenilin, a component of the γ-secretase complex, has been reported as a mol­ecular target of DAPT (Morohashi et al., 2006[Morohashi, Y., Kan, T., Tominari, Y., Fuwa, H., Okamura, Y., Watanabe, N., Sato, C., Natsugari, H., Fukuyama, T., Iwatsubo, T. & Tomita, T. (2006). J. Biol. Chem. 281, 14670-14676.]). Besides being a γ-secretase inhibitor, DAPT is also an inhibitor of the Notch signaling pathway, involved in cell proliferation, differentiation and apoptosis (Hansson et al., 2004[Hansson, E. M., Lendahl, U. & Chapman, G. (2004). Semin. Cancer Biol. 14, 320-328.]; Katoh & Katoh, 2007[Katoh, M. & Katoh, M. (2007). Int. J. Oncol. 30, 247-251.]). Due to this inhibition property, future clinical applications of DAPT for Alzheimer's disease treatment are rather unlikely. However, it is still widely used as a valuable tool in a variety of biomedical investigations (Sjolund et al., 2008[Sjolund, J., Johansson, M., Manna, S., Norin, C., Pietras, A., Beckman, S., Nilsson, E., Ljungberg, B. & Axelson, H. (2008). J. Clin. Invest. 118, 217-228.]; Bittner et al., 2009[Bittner, T., Fuhrmann, M., Burgold, S., Jung, C. K. E., Volbracht, C., Steiner, H., Mitteregger, G., Kretzschmar, H. A., Haass, C. & Herms, J. (2009). J. Neurosci. 29, 10405-10409.]; Huang et al., 2010[Huang, Y., Yang, X., Wu, Y., Jing, W., Cai, X., Tang, W., Liu, L., Liu, Y., Grottkau, B. E. & Lin, Y. (2010). Cell Prolif. 43, 147-156.]; Zhu et al., 2010[Zhu, F., Li, T., Qiu, F., Fan, J., Zhou, Q., Ding, X., Nie, J. & Yu, X. (2010). Am. J. Pathol. 176, 650-659.]), with new and inter­esting features and possible novel applications emerging (Grottkau et al., 2009[Grottkau, B. E., Chen, X., Friedrich, C. C., Yang, X., Jing, W., Wu, Y., Cai, X., Liu, Y., Huang, Y. & Lin, Y. (2009). Int. J. Oral Sci. 1, 81-89.]; Loane et al., 2009[Loane, D. J., Pocivavsek, A., Moussa, C., Thompson, R., Matsuoka, Y., aden, A. I., Rebeck, G. W. & Burns, M. P. (2009). Nat. Med. 15, 377-379.]). To facilitate the rational design of γ-secretase inhibitors with improved properties, we have crystallized and elucidated the structure of DAPT.

[Scheme 1]

The single mol­ecule of the DAPT dipeptide in the asymmetric unit of (I)[link] is in a compact conformation (Fig. 1[link]), in which the main-chain torsion angles lie in the allowed regions of the Ramachandran plot, viz. φ = −69.43 (17)° and ψ = −33.53 (18)° for Ala, and φ = −161.83 (14)° and ψ = 157.57 (13)° for PheGly, so that the former residue corresponds to the α-helical and the latter to the extended β-conformation.

There is only a single inter­molecular hydrogen bond between the Ala N20—H group and carbonyl atom O21 of the Ala residue related by translation parallel to a (Fig. 2[link]a). The remaining N and O atoms of DAPT are not engaged in hydrogen bonds.

All H atoms were identified from the difference Fourier synthesis. Two modes of their refinement were applied, firstly using the customary `riding' model in geometrically idealized positions utilizing the appropriate rigid-body constraints in SHELXL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), and secondly refining all their positional and isotropic U parameters without any constraints or restraints. The R(all) factors for such constrained and free refinements were comparable (0.0408 and 0.0399, respectively). The root-mean-square deviation (r.m.s.d.) of all 26 bond lengths to all H atoms between the two models was 0.036 Å and the r.m.s.d. of all bond directions was 4.0°, with only one outlier differing by 14.6° from the idealized bond direction. The single outlier corresponds to H201, an H atom of the amide N atom, which is engaged in the only (inter­molecular) hydrogen bond in the structure. Its distortion from the direction exactly bisecting the C11—N20—C22 angle is clearly caused by the tendency of the hydrogen bond to be linear (Fig. 2[link]b). Excluding it from the statistics of the bond directions resulted in an r.m.s.d. for the 25 bond directions of 2.8°. The model after the nonconstrained refinement of H atoms was accepted as the result of the SHELXL minimization.

The difference Fourier synthesis computed at the end of the SHELXL refinement showed relatively strong residual electron-density maxima located between bonded atoms (near bond centers) for almost all bonds. These features are due to bonding effects and their visibility is warranted by the combination of three facts: high data resolution, high model quality (low R factor) and low B factors (B < 5 Å2) (Afonine et al., 2004[Afonine, P. V., Lunin, V. Y., Muzet, N. & Urzhumtsev, A. (2004). Acta Cryst. D60, 260-274.]). A multipolar model (Hansen & Coppens, 1978[Hansen, N. K. & Coppens, P. (1978). Acta Cryst. A34, 909-921.]) is appropriate to use in such cases, since it accounts for the effects of atom inter­ations. It has been demonstrated that a simplified inter­atomic scatterers (IAS) model is capable of producing results of similar quality using fewer refinable parameters (Afonine et al., 2004[Afonine, P. V., Lunin, V. Y., Muzet, N. & Urzhumtsev, A. (2004). Acta Cryst. D60, 260-274.], 2007[Afonine, P. V., Grosse-Kunstleve, R. W., Adams, P. D., Lunin, V. Y. & Urzhumtsev, A. (2007). Acta Cryst. D63, 1194-1197.]). An additional refinement was therefore undertaken with the program PHENIX (Afonine et al., 2005[Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). CCP4 Newslett. 42, contribution 8.]), which supports refinement with the IAS option.

The PHENIX procedure started with the independent atom model (IAM), which included completely unrestrained refinement of atomic coordinates, anisotropic displacement parameters for non-H atoms and isotropic displacement parameters for H atoms. The occupancies of the H atoms were allowed to refine, to account for the possible effect of H-atom abstraction due to radiation damage (Meents et al., 2009[Meents, A., Dittrich, B. & Gutmann, S. (2009). J. Synchrotron Rad. 16, 183-190.]). This resulted in R(all) = 0.0411. For comparison, an analogous refinement was attempted where the only difference was that a riding model (of the same character as previously with SHELXL) was used for the H atoms instead of refining them freely. Refinement using a riding model resulted in an increased R(all) value of 0.0444. The model-phased residual (Fobs − Fcalc) map computed for the best IAM model (with H atoms refined freely) showed significant positive electron-density peaks around covalent bond centers for almost all bonds, as well as negative stick-like electron-density blobs at the centers of the aromatic rings oriented perpendicular to the ring plane (Fig. 3[link]a). These features were accounted for by the addition of IAS to those bonds that showed pronounced residual electron density, and their occupancies and isotropic displacement parameters were refined (anisotropic displacement parameters were refined for aromatic ring-centered IAS). This procedure resulted in R(all) = 0.0325 and considerably cleared up the difference density map (Fig. 3[link]b). The distribution of the values of the grid points of this map is shown in Fig. 4[link]. Before the introduction of IAS, the map values ranged between −0.214 and 0.266 eÅ−3 (r.m.s.d. = 0.063 e Å−3), and afterwards the map was flatter with a range of values between −0.155 and 0.154 e Å−3 (r.m.s.d. = 0.037 e Å−3). The results of the PHENIX refinement should be treated as final, but are presented in the Supplementary Material , since the refined parameters are not accompanied by standard uncertainties.

[Figure 1]
Figure 1
The mol­ecule of DAPT, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2]
Figure 2
(a) The packing of DAPT mol­ecules, viewed along the b direction. The only inter­molecular hydrogen bond is marked as dashed lines. (b) A close-up of the N20—H⋯O21 hydrogen bond, with atom H210 shown in two options, viz. in the calculated idealized position and after free refinement without constraints. The atom labeled O21 is a symmetry equivalent generated from atom O21 by the operator (1 + x, y, z). The difference map computed with atom H210 omitted from the structure-factor calculation is shown as a wire mesh.
[Figure 3]
Figure 3
(a) Difference Fourier map at 0.11/−0.15 e Å−3 contour levels (in the electronic version of the paper, blue denotes positive and red negative) before modeling inter­atomic scatterers in PHENIX. (b) Difference Fourier map after IAS refinement at the same contour levels. The positions of the inter­atomic scatterers (at the centers of the bonds and phenyl rings) are marked as spheres of arbitrary radii, in addition to all atoms.
[Figure 4]
Figure 4
The distribution of the values of the residual difference map before (upper curve) and after (lower curve) the introduction of IAS into the refined model. The graph shows the fraction of map grid points within ten ranges of the density values in the whole map.

Experimental

DAPT was prepared according to the general synthetic procedure reported by Kan et al. (2004[Kan, T., Tominari, Y., Rikimaru, K., Morohashi, Y., Natsugari, H., Tomita, T., Iwatsubo, T. & Fukuyama, T. (2004). Bioorg. Med. Chem. Lett. 14, 1983-1985.]), and a 64% overall yield was obtained. The crude product was purified using preparative high-pressure liquid chromatography, followed by crystallization from a 1:1 mixture of acetonitrile and water.

A needle-like crystal of (I)[link] elongated along a was selected, picked up in a rayon loop and quickly cryo-cooled in a stream of cold nitro­gen gas at the single-axis goniostat of the SERCAT synchrotron station 22ID at the Advanced Photon Source, Argonne National Laboratory, USA. Diffraction images were collected using a Mar­research MAR300 CCD detector in four passes differing in their effective exposure and resolution limits, in order to measure adequately the weakest high-resolution reflections as well as the strongest low-angle reflections without overloading the detector pixels. All 53285 measured intensities from all passes were scaled and merged together into the set of 3216 unique reflections with an overall Rmerge factor of 0.061. The data set is rather strong, with an I/σ(I) ratio of 38 at the highest resolution of 0.72 Å.

Crystal data

  • C23H26F2N2O4

  • Mr = 432.46

  • Orthorhombic, P 21 21 21

  • a = 5.490 (5) Å

  • b = 15.720 (15) Å

  • c = 24.82 (2) Å

  • V = 2142 (4) Å3

  • Z = 4

  • Synchrotron radiation

  • λ = 0.70000 Å

  • μ = 0.10 mm−1

  • T = 100 K

  • 0.25 × 0.05 × 0.04 mm
Data collection

  • Marresearch MAR300 CCD diffractometer

  • Absorption correction: multi-scan (SCALEPACK; Otwinowski et al., 2003[Otwinowski, Z., Borek, D., Majewski, W. & Minor, W. (2003). Acta Cryst. A59, 228-234.]) Tmin = 0.974, Tmax = 0.996

  • 3216 measured reflections

  • 3216 independent reflections

  • 3157 reflections with I > 2σ(I)

  • Rint = 0.061
Refinement

  • R[F2 > 2σ(F2)] = 0.040

  • wR(F2) = 0.112

  • S = 1.10

  • 3216 reflections

  • 384 parameters

  • All H-atom parameters refined

  • Δρmax = 0.35 e Å−3

  • Δρmin = −0.23 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N20—H201⋯O21i 0.92 (4) 2.03 (3) 2.933 (3) 165 (3)
Symmetry code: (i) x+1, y, z.

The H atoms were located in a difference synthesis and refined without restraints.

The PHENIX (Afonine et al., 2005[Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005). CCP4 Newslett. 42, contribution 8.]) refinement was performed using a direct summation algorithm for structure-factor and gradient calculation (as opposed to using a fast Fourier transform) and using a maximum-likelihood refinement target (Lunin et al., 2002[Lunin, V. Y., Afonine, P. V. & Urzhumtsev, A. G. (2002). Acta Cryst. A58, 270-282.]). Waasmaier & Kirfel (1995[Waasmaier, D. & Kirfel, A. (1995). Acta Cryst. A51, 416-431.]) approximation to the standard form factors was used. The form factors for IAS are distributed as part of cctbx (Grosse-Kunstleve et al., 2002[Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. (2002). J. Appl. Cryst. 35, 126-136.]).

Data collection: SERGUI (SERCAT APS beamline software); cell refinement: HKL-2000 (Otwinowski & Minor, 1997[Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307-326. New York: Academic Press.]); data reduction: HKL-2000; program(s) used to solve structure: SHELXD (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and pyMOL (DeLano, 2002[DeLano, W. L. (2002). The pyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.]); software used to prepare material for publication: ORTEP-3 and pyMOL.

Supporting information

Crystal structure: contains datablocks global, I, phenix. DOI: 10.1107/S0108270110044136/mx3037sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S0108270110044136/mx3037Isup2.hkl

Structure factors: contains datablock . DOI: 10.1107/S0108270110044136/mx3037phenixsup3.hkl


Comment top

Alzheimer's disease, a progressive neurodegenerative disorder, is the most prominent contributor to senile dementia, a condition affecting millions of individuals worldwide. The disease is associated with the presence of extracellular plaques and intracellular neurofibrillary tangles in the brains of Alzheimer's sufferers (Goedert & Spillantini, 2006). Amyloid-β plaque peptides are produced as a result of the sequential proteolytic cleavages of a protein precursor, involving β- and γ-secretase enzymes (Chapman et al., 2001). A great amount of effort has been spent in exploring the use of the enzyme inhibitors and modulators aimed at preventing amyloid formation (Wolfe, 2008). An approach based on targeting γ-secretase (Roberts, 2002; Barten et al., 2006; Tomita, 2008) seems to be more promising (Wolfe, 2008) than an approach that has been focused on β-secretase (Vassar, 2002; Schmidt et al., 2006). This research generated a number of potent and specific inhibitors, among them N-[N-(3,5-difluorophenylacetyl)-S-alanyl]-(S)- phenylglycine tert-butyl ester (DAPT) (Dovey et al., 2001). DAPT, (I), has been shown to block amyloid-β production in human neuronal cultures, and its administration to transgenic mice resulted in the first successful reduction of amyloid level in vivo (Dovey et al., 2001; Lanz et al., 2003). Presenilin, a component of the γ-secretase complex, has been reported as a molecular target of DAPT (Morohashi et al., 2006). Besides being a γ-secretase inhibitor, DAPT is also an inhibitor of the Notch signaling pathway, involved in cell proliferation, differentiation and apoptosis (Hansson et al., 2004; Katoh & Katoh, 2007). Due to this inhibition property, future clinical applications of DAPT for Alzheimer's disease treatment are rather unlikely. However, it is still widely used as a valuable tool in a variety of biomedical investigations (Sjolund et al., 2008; Bittner et al., 2009; Huang et al., 2010; Zhu et al., 2010), with new and interesting features and possible novel applications emerging (Grottkau et al., 2009; Loane et al., 2009).

The single molecule of DAPT dipeptide in the asymmetric unit of (I) is in a compact conformation (Fig. 1), in which the main-chain torsion angles lie in the allowed regions of the Ramachandran plot, ϕ = -69.5°, ψ = 33.6° for Ala and ϕ= -161.7°, ψ = 157.6° for PheGly, so that the former residue corresponds to the α-helical and the latter to the extended β-conformation.

There is only a single intermolecular hydrogen bond between the Ala N20—H group and carbonyl atom O21 of the Ala residue related by translation parallel to a (Fig. 2a). The remaining N and O atoms of DAPT are not engaged in hydrogen bonds.

All H atoms were identified from the difference Fourier synthesis. Two modes of their refinement were applied, firstly using the customary `riding' model in geometrically idealized positions utilizing the appropriate rigid-body constraints in SHELXL (Sheldrick, 2008), and secondly refining all their positional and isotropic U parameters without any constraints or restraints. The R(all) factors for such constrained and free refinement were comparable (0.0408 and 0.0399, respectively). The root mean-square deviation (r.m.s.d.) of all 26 bond lengths to all H atoms between the two models was 0.036 Å and the r.m.s.d. of all bond directions was 4.0°, with only one outlier differing by 14.6° from the idealized bond direction. The single outlier corresponds to H201, an H atom of the amide N atom, which is engaged in the only (intermolecular) hydrogen bond in the structure. Its distortion from the direction exactly bisecting the C11—N20—C22 angle is clearly caused by the tendency of the hydrogen bond to be linear (Fig. 2b). Excluding it from the statistics of the bond directions resulted in an r.m.s.d. for the 25 bond directions of 2.8°. The model after the non-constrained refinement of H atoms was accepted as the result of the SHELXL minimization.

The difference Fourier synthesis computed at the end of the SHELXL refinement showed relatively strong residual density maxima located between bonded atoms (near bond centers) for almost all bonds.These features are due to bonding effects and their visibility is warranted by the combination of three facts: high resolution of the data, high model quality (low R factor) and low B factors (B < 5 Å2) (Afonine et al., 2004). A multipolar model (Hansen & Coppens, 1978) is appropriate to use in such cases, since it accounts for the effects of atom interations. It has been demonstrated that a simplified interatomic scatterers (IAS) model is capable of producing results of similar quality using fewer refinable parameters (Afonine et al., 2004, 2007). An additional refinement was therefore undertaken with the program PHENIX (Afonine et al., 2005), which supports refinement with the IAS option.

The PHENIX procedure started with the independent atom model (IAM), which included completely unrestrained refinement of coordinates, anisotropic displacement parameters for non-H atoms and isotropic displacement parameters for H atoms. The occupancies of the H atoms were allowed to refine, to account for the possible effect of H-atom abstraction due to radiation damage (Meents et al., 2009). This resulted in R(all) = 0.0411. For comparison, an analogous refinement was attempted where the only difference was that a riding model (of the same character as previously with SHELXL) was used for the H atoms instead of refining them freely. Refinement using a riding model resulted in an increased R(all) of 0.0444. The model-phased residual (Fobs - Fcalc) map computed for the best IAM model (with H atoms refined freely) showed significant positive electron-density peaks around covalent bond centers for almost all bonds, as well as negative stick-like electron-density blobs at the centers of the aromatic rings oriented perpendicular to the ring plane (Fig. 3a). These features were accounted for by the addition of IAS to those bonds that showed pronounced residual electron density, and their occupancies and isotropic displacement parameters were refined (anisotropic displacement parameters were refined for aromatic ring-centered IAS). This procedure resulted in R(all) = 0.0325 and considerably cleared up the difference density map (Fig. 3b). The distribution of the values of the grid points of this map is shown in Fig. 4. Before the introduction of IAS, the map values ranged between -0.214 and 0.266 eÅ-3 (r.m.s.d. 0.063 e Å-3), and afterwards the map was flatter with a range of values between -0.155 and 0.154 e Å-3 (r.m.s.d. 0.037 e Å-3). The results of the PHENIX refinement should be treated as final, but are presented in the Supplementary Material, since the refined parameters are not accompanied by standard uncertainties.

Experimental top

DAPT was prepared according to the general synthetic scheme reported by Kan et al. (2004), and a 64% overall yield was obtained. The crude product was purified using preparative high-pressure liquid chromatography, followed by crystallization from a 1:1 mixture of acetonitrile and water.

A needle-like crystal of (I) elongated along a was selected, picked up in a rayon loop and quickly cryo-cooled in a stream of cold nitrogen gas at the single-axis goniostat of the SERCAT synchrotron station 22ID at the Advanced Photon Source, Argonne National Laboratory, USA. Diffraction images were collected using a Marresearch MAR300 CCD detector in four passes differing in their effective exposure and resolution limits, in order to measure adequately the weakest high-resolution reflections as well as the strongest low-angle ones without overloading the detector pixels. All 53285 measured intensities from all passes were scaled and merged together into the set of 3216 unique reflections with an overall Rmerge factor of 0.061. The data set is rather strong, with an I/σ(I) ratio of 38 at the highest resolution of 0.72 Å.

Refinement top

The structure was solved with SHELXD and refined with SHELXL (Sheldrick, 2008) to R[F2>2σ(F2)] = 0.0395 and R1(all) = 0.0399. The H atoms were located in a difference synthesis (Fig. 3a) and refined without restraints.

The PHENIX (Afonine et al., 2005) refinement was performed using a direct summation algorithm for structure-factor and gradient calculation (as opposed to using a fast Fourier transform) and using a maximum-likelihood refinement target (Lunin et al., 2002). Waasmaier & Kirfel (1995) approximation to the standard form factors was used. The form factors for IAS are distributed as part of cctbx (Grosse-Kunstleve et al., 2002).

Computing details top

Data collection: SERGUI, SERCAT APS beamline software for (I). Cell refinement: HKL-2000 (Otwinowski & Minor, 1997) for (I). Data reduction: HKL-2000 (Otwinowski & Minor, 1997) for (I). Program(s) used to solve structure: SHELXD (Sheldrick, 2008) for (I). Program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) for (I). Molecular graphics: ORTEP-3 (Farrugia, 1997) and pyMOL (DeLano, 2002) for (I). Software used to prepare material for publication: ORTEP-3 (Farrugia, 1997) and pyMOL (DeLano, 2002) for (I).

Figures top
[Figure 1] Fig. 1. The molecule of DAPT, showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. (a) The packing of DAPT molecules, viewed along the b direction. The only intermolecular hydrogen bond is marked as dashed lines. (b) A close-up of the N20—H···O21 hydrogen bond, with atom H210 shown in two options, in the calculated idealized position and after free refinement without constraints. The atom labeled O21 is a symmetry equivalent generated from atom O21 by the operator (1 + x, y, z). The difference map computed with atom H210 omitted from the structure-factor calculation is shown as a wire mesh.
[Figure 3] Fig. 3. (a) Difference Fourier map at 0.11/-0.15 e Å-3 contour levels (in the electronic version of the journal, blue denotes positive and red negative) before modeling interatomic scatterers in PHENIX. (b) Difference Fourier map after IAS refinement at the same contour levels. The positions of the interatomic scatterers (at the centers of the bonds and phenyl rings) are marked as spheres of arbitrary radii, in addition to all atoms.
[Figure 4] Fig. 4. The distribution of the values of the residual difference map before (upper curve) and after (lower curve) the introduction of IAS into the refined model. The graph shows the fraction of map grid points within ten ranges of the density values in the whole map.
(I) N-{N-[2-(3,5-Difluorophenyl)acetyl]-(S)-alanyl}- (S)-phenylglycine tert-butyl ester top
Crystal data top
C23H26F2N2O4F(000) = 912
Mr = 432.46Dx = 1.341 Mg m−3
Orthorhombic, P212121Synchrotron radiation, λ = 0.70000 Å
a = 5.490 (5) Åθ = 1.5–29.1°
b = 15.720 (15) ŵ = 0.10 mm−1
c = 24.82 (2) ÅT = 100 K
V = 2142 (4) Å3Needle, colourless
Z = 40.25 × 0.05 × 0.04 mm
Data collection top
Marresearch MAR300 CCD
diffractometer		3216 independent reflections
Radiation source: SERCAT 22ID synchrotron beamline, APS, USA3157 reflections with I > 2σ(I)
Si111 double crystal monochromatorRint = 0.061
ω scansθmax = 29.1°, θmin = 1.5°
Absorption correction: multi-scan
(SCALEPACK; Otwinowski et al., 2003)		h = 0→6
Tmin = 0.974, Tmax = 0.996k = 0→21
3216 measured reflectionsl = 0→33
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.112All H-atom parameters refined
S = 1.10 w = 1/[σ2(Fo2) + (0.0854P)2 + 0.2521P]
where P = (Fo2 + 2Fc2)/3
3216 reflections(Δ/σ)max < 0.001
384 parametersΔρmax = 0.35 e Å−3
0 restraintsΔρmin = −0.23 e Å−3
Crystal data top
C23H26F2N2O4V = 2142 (4) Å3
Mr = 432.46Z = 4
Orthorhombic, P212121Synchrotron radiation, λ = 0.70000 Å
a = 5.490 (5) ŵ = 0.10 mm−1
b = 15.720 (15) ÅT = 100 K
c = 24.82 (2) Å0.25 × 0.05 × 0.04 mm
Data collection top
Marresearch MAR300 CCD
diffractometer		3216 independent reflections
Absorption correction: multi-scan
(SCALEPACK; Otwinowski et al., 2003)		3157 reflections with I > 2σ(I)
Tmin = 0.974, Tmax = 0.996Rint = 0.061
3216 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0400 restraints
wR(F2) = 0.112All H-atom parameters refined
S = 1.10Δρmax = 0.35 e Å−3
3216 reflectionsΔρmin = −0.23 e Å−3
384 parameters
Special details top

Experimental. diffraction data were measured at the station 22ID of the APS synchrotron by rotation method a in three sweeps of different exposure and all data were scaled and merged ino one data set

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*/Ueq
C110.6539 (3)0.28035 (9)0.30106 (5)0.0201 (3)
O110.4447 (2)0.27996 (8)0.28339 (5)0.0256 (3)
C120.8693 (3)0.30527 (10)0.26642 (6)0.0233 (3)
H1210.853 (5)0.2715 (15)0.2341 (10)0.032 (6)*
H1221.016 (5)0.2923 (16)0.2835 (10)0.030 (6)*
C130.8620 (3)0.39950 (9)0.25378 (5)0.0211 (3)
C141.0419 (3)0.45296 (10)0.27404 (6)0.0248 (3)
H1411.167 (6)0.4343 (16)0.2930 (10)0.036 (7)*
C151.0266 (4)0.53925 (11)0.26319 (6)0.0279 (4)
F151.2001 (3)0.59119 (7)0.28355 (5)0.0390 (3)
C160.8429 (4)0.57523 (10)0.23277 (6)0.0270 (3)
H1610.831 (6)0.6349 (16)0.2259 (10)0.034 (6)*
C170.6696 (4)0.51989 (10)0.21324 (6)0.0249 (3)
F170.4878 (2)0.55269 (7)0.18267 (4)0.0343 (3)
C180.6721 (3)0.43342 (10)0.22280 (6)0.0236 (3)
H1810.553 (6)0.3990 (17)0.2092 (10)0.036 (6)*
C210.3526 (3)0.32386 (9)0.40160 (6)0.0196 (3)
O210.1333 (2)0.32019 (7)0.41180 (5)0.0248 (3)
C220.5011 (3)0.24373 (9)0.38930 (6)0.0202 (3)
H2210.393 (6)0.2058 (15)0.3702 (10)0.034 (6)*
N200.7020 (3)0.26076 (8)0.35303 (5)0.0208 (3)
H2010.852 (6)0.2726 (17)0.3679 (11)0.042 (7)*
C230.5961 (4)0.20635 (10)0.44195 (6)0.0276 (4)
H2310.468 (5)0.1985 (15)0.4680 (10)0.031 (6)*
H2320.719 (5)0.2452 (15)0.4603 (9)0.026 (5)*
H2330.678 (6)0.1537 (17)0.4349 (10)0.037 (6)*
C310.5399 (3)0.54795 (9)0.40207 (6)0.0219 (3)
O310.7531 (3)0.53848 (7)0.39163 (5)0.0267 (3)
C320.3781 (3)0.47558 (9)0.42252 (6)0.0217 (3)
H3210.214 (4)0.4849 (12)0.4083 (8)0.014 (4)*
N300.4815 (3)0.39654 (8)0.40330 (6)0.0229 (3)
H3010.639 (8)0.396 (2)0.3937 (14)0.062 (10)*
C330.3839 (3)0.48287 (9)0.48414 (6)0.0211 (3)
C340.1976 (4)0.52431 (10)0.51115 (7)0.0265 (3)
H3410.051 (5)0.5420 (16)0.4905 (10)0.034 (6)*
C350.2105 (4)0.53464 (10)0.56697 (7)0.0315 (4)
H3510.082 (6)0.5656 (17)0.5835 (11)0.041 (7)*
C360.4094 (4)0.50469 (11)0.59552 (7)0.0305 (4)
H3610.420 (5)0.5126 (15)0.6362 (10)0.035 (6)*
C370.5960 (4)0.46317 (12)0.56849 (7)0.0304 (4)
H3710.729 (6)0.4426 (17)0.5879 (10)0.034 (6)*
C380.5831 (4)0.45218 (11)0.51271 (7)0.0265 (3)
H3810.719 (6)0.4225 (16)0.4938 (11)0.037 (7)*
O400.4132 (2)0.61970 (6)0.40121 (4)0.0210 (2)
C400.5361 (3)0.70330 (9)0.39555 (6)0.0203 (3)
C410.6757 (4)0.70880 (11)0.34279 (6)0.0270 (3)
H4110.569 (6)0.6977 (18)0.3116 (12)0.046 (7)*
H4120.801 (6)0.6698 (17)0.3424 (10)0.038 (7)*
H4130.738 (5)0.7686 (15)0.3396 (9)0.033 (6)*
C420.3215 (4)0.76394 (10)0.39591 (7)0.0276 (3)
H4210.385 (6)0.8219 (17)0.3924 (11)0.043 (7)*
H4220.202 (7)0.7472 (19)0.3670 (12)0.050 (8)*
H4230.234 (6)0.7637 (19)0.4307 (11)0.042 (7)*
C430.6977 (4)0.71596 (11)0.44472 (6)0.0273 (3)
H4310.752 (5)0.7734 (16)0.4444 (10)0.032 (6)*
H4320.600 (6)0.7031 (15)0.4796 (10)0.035 (6)*
H4330.835 (5)0.6775 (15)0.4437 (9)0.027 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C110.0221 (8)0.0188 (5)0.0195 (6)−0.0010 (5)0.0003 (5)−0.0024 (5)
O110.0213 (6)0.0326 (6)0.0229 (5)−0.0019 (5)−0.0027 (4)0.0007 (4)
C120.0220 (8)0.0240 (6)0.0240 (6)0.0003 (6)0.0041 (6)−0.0019 (5)
C130.0213 (8)0.0236 (6)0.0183 (5)−0.0014 (5)0.0023 (5)−0.0015 (5)
C140.0227 (9)0.0288 (7)0.0229 (6)−0.0016 (6)−0.0015 (6)−0.0034 (5)
C150.0283 (10)0.0287 (7)0.0266 (7)−0.0063 (7)0.0001 (6)−0.0068 (6)
F150.0377 (7)0.0323 (5)0.0469 (6)−0.0106 (5)−0.0104 (5)−0.0087 (5)
C160.0324 (10)0.0239 (7)0.0246 (6)−0.0038 (6)0.0009 (6)−0.0006 (5)
C170.0271 (9)0.0284 (7)0.0191 (6)−0.0006 (6)−0.0016 (6)0.0025 (5)
F170.0370 (7)0.0337 (5)0.0322 (5)0.0001 (5)−0.0109 (5)0.0087 (4)
C180.0247 (9)0.0266 (7)0.0196 (6)−0.0038 (6)−0.0007 (6)−0.0008 (5)
C210.0238 (8)0.0169 (5)0.0181 (5)−0.0026 (5)−0.0008 (5)0.0009 (4)
O210.0237 (7)0.0232 (5)0.0277 (5)−0.0031 (4)−0.0006 (5)−0.0002 (4)
C220.0236 (8)0.0166 (5)0.0205 (6)−0.0031 (5)−0.0010 (5)0.0001 (5)
N200.0204 (7)0.0215 (5)0.0206 (5)−0.0020 (5)−0.0018 (5)−0.0002 (4)
C230.0384 (11)0.0221 (6)0.0224 (6)0.0005 (7)−0.0018 (6)0.0051 (5)
C310.0275 (9)0.0174 (6)0.0208 (6)−0.0029 (6)−0.0001 (6)−0.0007 (5)
O310.0253 (7)0.0207 (5)0.0341 (6)−0.0017 (5)0.0051 (5)0.0004 (4)
C320.0244 (8)0.0154 (5)0.0253 (6)−0.0021 (5)0.0000 (6)−0.0001 (5)
N300.0236 (8)0.0164 (5)0.0288 (6)−0.0038 (5)0.0032 (5)−0.0031 (4)
C330.0246 (8)0.0140 (5)0.0246 (6)−0.0019 (5)0.0030 (6)0.0015 (4)
C340.0281 (9)0.0191 (6)0.0324 (7)0.0042 (6)0.0051 (7)0.0030 (5)
C350.0376 (11)0.0228 (7)0.0339 (8)0.0040 (7)0.0090 (7)−0.0024 (6)
C360.0381 (11)0.0271 (7)0.0262 (7)−0.0039 (7)0.0045 (7)−0.0022 (6)
C370.0300 (10)0.0339 (8)0.0272 (7)−0.0004 (7)−0.0016 (6)0.0016 (6)
C380.0252 (9)0.0266 (7)0.0275 (7)0.0021 (6)0.0018 (6)−0.0005 (6)
O400.0235 (6)0.0160 (4)0.0234 (5)−0.0033 (4)−0.0009 (4)0.0017 (3)
C400.0239 (8)0.0168 (5)0.0202 (5)−0.0045 (5)−0.0030 (5)0.0009 (4)
C410.0292 (9)0.0292 (7)0.0226 (6)−0.0039 (7)0.0024 (6)0.0063 (6)
C420.0263 (9)0.0198 (6)0.0366 (8)−0.0015 (6)−0.0025 (7)0.0014 (5)
C430.0298 (10)0.0280 (7)0.0242 (6)−0.0034 (7)−0.0070 (6)−0.0036 (6)
Geometric parameters (Å, º) top
C11—O111.229 (2)C31—C321.530 (2)
C11—N201.352 (2)C32—N301.447 (2)
C11—C121.514 (3)C32—C331.534 (3)
C12—C131.515 (3)C32—H3210.98 (2)
C12—H1210.97 (2)N30—H3010.90 (4)
C12—H1220.93 (3)C33—C381.390 (3)
C13—C141.391 (2)C33—C341.386 (2)
C13—C181.401 (2)C34—C351.397 (3)
C14—C151.385 (3)C34—H3411.00 (3)
C14—H1410.89 (3)C35—C361.384 (3)
C15—F151.352 (2)C35—H3510.95 (3)
C15—C161.381 (3)C36—C371.388 (3)
C16—C171.377 (3)C36—H3611.02 (3)
C16—H1610.95 (2)C37—C381.397 (3)
C17—F171.356 (2)C37—H3710.93 (3)
C17—C181.380 (3)C38—H3811.00 (3)
C18—H1810.92 (3)O40—C401.484 (2)
C21—O211.232 (3)C40—C421.516 (3)
C21—N301.344 (2)C40—C411.520 (2)
C21—C221.531 (2)C40—C431.522 (2)
C22—N201.449 (2)C41—H4110.99 (3)
C22—C231.525 (2)C41—H4120.92 (3)
C22—H2210.97 (3)C41—H4131.00 (2)
N20—H2010.92 (3)C42—H4210.98 (3)
C23—H2310.96 (3)C42—H4221.01 (3)
C23—H2321.02 (3)C42—H4230.99 (3)
C23—H2330.96 (3)C43—H4310.95 (3)
C31—O311.208 (3)C43—H4321.04 (3)
C31—O401.325 (2)C43—H4330.97 (3)
O11—C11—N20121.46 (15)C31—C32—C33105.25 (13)
O11—C11—C12121.90 (15)N30—C32—H321111.8 (12)
N20—C11—C12116.61 (16)C31—C32—H321107.7 (12)
C13—C12—C11110.49 (14)C33—C32—H321111.5 (12)
C13—C12—H121111.3 (14)C21—N30—C32122.26 (16)
C11—C12—H121104.9 (17)C21—N30—H301120 (2)
C13—C12—H122109.3 (16)C32—N30—H301118 (2)
C11—C12—H122111.1 (16)C38—C33—C34119.80 (16)
H121—C12—H122110 (2)C38—C33—C32119.96 (15)
C14—C13—C18119.80 (15)C34—C33—C32120.14 (15)
C14—C13—C12119.82 (16)C33—C34—C35119.82 (18)
C18—C13—C12120.37 (15)C33—C34—H341118.8 (15)
C15—C14—C13118.58 (17)C35—C34—H341121.2 (15)
C15—C14—H141118.4 (17)C36—C35—C34120.54 (18)
C13—C14—H141123.1 (17)C36—C35—H351122.7 (17)
F15—C15—C16118.12 (16)C34—C35—H351116.7 (17)
F15—C15—C14118.41 (17)C37—C36—C35119.66 (17)
C16—C15—C14123.47 (16)C37—C36—H361119.5 (16)
C17—C16—C15115.99 (16)C35—C36—H361120.9 (16)
C17—C16—H161120.8 (18)C36—C37—C38119.99 (19)
C15—C16—H161123.2 (18)C36—C37—H371119.5 (16)
F17—C17—C16117.73 (16)C38—C37—H371120.5 (17)
F17—C17—C18118.56 (16)C33—C38—C37120.19 (17)
C16—C17—C18123.70 (17)C33—C38—H381120.7 (16)
C17—C18—C13118.46 (16)C37—C38—H381119.1 (16)
C17—C18—H181120.8 (17)C31—O40—C40121.11 (15)
C13—C18—H181120.8 (17)O40—C40—C42101.71 (15)
O21—C21—N30123.21 (16)O40—C40—C41111.18 (12)
O21—C21—C22121.52 (15)C42—C40—C41111.18 (14)
N30—C21—C22115.18 (16)O40—C40—C43107.75 (12)
N20—C22—C23110.07 (16)C42—C40—C43111.48 (14)
N20—C22—C21112.17 (13)C41—C40—C43112.93 (17)
C23—C22—C21109.15 (13)C40—C41—H411111.4 (19)
N20—C22—H221106.1 (16)C40—C41—H412110.3 (16)
C23—C22—H221113.2 (15)H411—C41—H412109 (2)
C21—C22—H221106.2 (17)C40—C41—H413107.1 (14)
C11—N20—C22119.06 (15)H411—C41—H413108 (2)
C11—N20—H201120.6 (18)H412—C41—H413112 (2)
C22—N20—H201118.0 (18)C40—C42—H421108 (2)
C22—C23—H231112.0 (16)C40—C42—H422109.8 (18)
C22—C23—H232112.3 (13)H421—C42—H422114 (2)
H231—C23—H232105.2 (19)C40—C42—H423112.5 (18)
C22—C23—H233109.7 (15)H421—C42—H423105 (2)
H231—C23—H233111 (2)H422—C42—H423108 (3)
H232—C23—H233107 (2)C40—C43—H431107.4 (15)
O31—C31—O40127.59 (15)C40—C43—H432110.0 (17)
O31—C31—C32122.83 (15)H431—C43—H432111 (2)
O40—C31—C32109.47 (16)C40—C43—H433110.6 (14)
N30—C32—C31107.54 (15)H431—C43—H433110 (2)
N30—C32—C33112.62 (13)H432—C43—H433108 (2)
O11—C11—C12—C1369.49 (19)O40—C31—C32—N30157.57 (13)
N20—C11—C12—C13−108.71 (15)O31—C31—C32—C3394.25 (18)
C11—C12—C13—C14114.09 (18)O40—C31—C32—C33−82.15 (16)
C11—C12—C13—C18−64.48 (19)O21—C21—N30—C326.3 (2)
C18—C13—C14—C150.5 (2)C22—C21—N30—C32−170.14 (13)
C12—C13—C14—C15−178.07 (15)C31—C32—N30—C21−161.83 (14)
C13—C14—C15—F15179.15 (15)C33—C32—N30—C2182.7 (2)
C13—C14—C15—C16−0.7 (3)N30—C32—C33—C3838.0 (2)
F15—C15—C16—C17−179.56 (15)C31—C32—C33—C38−78.90 (18)
C14—C15—C16—C170.3 (3)N30—C32—C33—C34−145.73 (15)
C15—C16—C17—F17−179.28 (15)C31—C32—C33—C3497.40 (19)
C15—C16—C17—C180.3 (3)C38—C33—C34—C35−0.3 (2)
F17—C17—C18—C13179.13 (14)C32—C33—C34—C35−176.63 (15)
C16—C17—C18—C13−0.5 (3)C33—C34—C35—C360.8 (3)
C14—C13—C18—C170.0 (2)C34—C35—C36—C37−0.8 (3)
C12—C13—C18—C17178.60 (14)C35—C36—C37—C380.3 (3)
O21—C21—C22—N20149.97 (14)C34—C33—C38—C37−0.1 (2)
N30—C21—C22—N20−33.53 (18)C32—C33—C38—C37176.19 (16)
O21—C21—C22—C23−87.76 (19)C36—C37—C38—C330.1 (3)
N30—C21—C22—C2388.74 (17)O31—C31—O40—C40−10.6 (2)
O11—C11—N20—C22−3.6 (2)C32—C31—O40—C40165.54 (12)
C12—C11—N20—C22174.62 (12)C31—O40—C40—C42179.27 (13)
C23—C22—N20—C11168.83 (13)C31—O40—C40—C4160.84 (18)
C21—C22—N20—C11−69.43 (17)C31—O40—C40—C43−63.41 (18)
O31—C31—C32—N30−26.0 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N20—H201···O21i0.92 (4)2.03 (3)2.933 (3)165 (3)
Symmetry code: (i) x+1, y, z.
(phenix) top
Crystal data top
?c = 24.82 Å
Mr = ?V = ? Å3
Orthorhombic, P212121Z = ?
a = 5.49 Å? radiation, λ = ? Å
b = 15.72 Å × × mm
Data collection top
h = ?→?l = ?→?
k = ?→?
Refinement top
Crystal data top
?c = 24.82 Å
Mr = ?V = ? Å3
Orthorhombic, P212121Z = ?
a = 5.49 Å? radiation, λ = ? Å
b = 15.72 Å × × mm
Data collection top
Refinement top
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
C110.6537860.2803270.3010970.021554
O110.4447980.2799320.2832920.0267360.983
C120.8693440.3051280.2663690.0249960.987
H1210.8546840.2713230.2331220.013159
H1221.0131420.2912860.2818780.015870
C130.8616380.3994240.2538190.0208840.970
C141.0421760.4530080.2741350.0260110.992
H1411.1757920.4307450.2956410.019966
C151.0268490.5394760.2631730.0283600.985
F151.1999020.5911240.2835860.0396660.976
C160.8424250.5755580.2326530.0271550.971
H1610.8284960.6343300.2268480.014640
C170.6690530.5197730.2132020.0255750.983
F170.4876920.5525800.1826720.0348530.979
C180.6718700.4331850.2227190.0245680.988
H1810.5425770.3974510.2102490.011054
C210.3538340.3237600.4015150.0196240.965
O210.1330610.3202320.4118340.0240580.958
C220.5010390.2436460.3892920.0206830.971
H2210.3888420.2059610.3729850.004120
N200.7021870.2607490.3531030.0216940.981
H2010.8362290.2694000.3674450.014438
C230.5955140.2061610.4419110.0288550.988
H2310.4663980.1999810.4685310.021642
H2320.7170590.2456150.4577670.012924
H2330.6761850.1523720.4350170.016243
C310.5393410.5479900.4019710.0227730.989
O310.7535670.5383380.3915600.0278470.973
C320.3780820.4756900.4225570.0224420.979
H3210.2136250.4849880.4084880.006355
N300.4812590.3966230.4032700.0245340.990
H3010.6269860.3968100.3939120.022370
C330.3838890.4827150.4839290.0219080.988
C340.1974940.5243980.5111010.0275530.983
H3410.0561290.5431550.4910990.016134
C350.2108780.5346320.5669180.0310620.969
H3510.0759520.5595720.5864790.026066
C360.4101760.5045060.5958160.0301510.956
H3610.4193310.5111750.6328120.015617
C370.5956640.4629500.5684500.0306730.962
H3710.7332510.4368400.5873310.011873
C380.5826610.4520500.5126870.0265560.962
H3810.7115310.4231910.4936050.012720
O400.4133620.6200000.4012280.0219080.978
C400.5364100.7032310.3955980.0206140.976
C410.6750590.7087890.3428760.0281290.987
H4110.5788540.6977450.3131130.012189
H4120.8021690.6709080.3412960.011793
H4130.7274110.7662390.3389080.020955
C420.3217610.7640170.3958390.0285460.971
H4210.3829240.8215990.3902580.019891
H4220.2147430.7499500.3671930.013121
H4230.2276070.7592850.4296880.012847
C430.6975550.7159520.4446910.0284650.990
H4310.7615120.7745380.4441990.008953
H4320.5987480.7035630.4764360.019884
H4330.8338850.6788860.4441330.019150
IS10.5419900.2801070.2915700.1266510.586
IS20.7497910.2913800.2856440.0436690.874
IS30.6838540.2681790.3333280.051617
IS40.8658810.3475790.2607190.067507
IS50.9581750.4281050.2646840.0513140.752
IS60.7715720.4154620.2390520.046530
IS71.0338250.5001230.2681660.063483
IS81.1246700.5686350.2747140.0340350.375
IS90.9171700.5609060.2450350.061699
IS100.7497190.5456760.2222600.062619
IS110.5829450.5353310.1986970.0464890.460
IS120.6707130.4721460.2184430.066325
IS130.2499430.3220980.4063690.0210460.517
IS140.4375060.2780980.3945590.041517
IS150.4185900.3609170.4024220.0110720.420
IS160.6055950.2525410.3704680.0073230.403
IS170.5501070.2241580.4166520.041522
IS180.6668260.5422430.3957670.0415720.432
IS190.4587140.5118400.4122630.0586300.794
IS200.4588020.5940260.4014950.0327600.910
IS210.4369060.4306280.4115740.0461180.538
IS220.3810210.4792430.4535480.052223
IS230.2916320.5033490.4973800.0468510.979
IS240.4951390.4655460.5000380.0416510.599
IS250.2037830.5291610.5370490.0526400.860
IS260.3244440.5174630.5833710.0378550.813
IS270.5000850.4843570.5825280.0456760.716
IS280.5883450.4568540.5372230.076387
IS290.4823110.6665650.3980800.0358430.363
IS300.6029570.7058920.3702980.0237670.864
IS310.4204810.7360500.3957300.0348500.411
IS320.6249680.7102340.4225950.0239280.721
IS330.8520490.4874660.2432490.240326
IS340.3969520.4936110.5398620.305167
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C110.0304040.0141350.020122−0.0009660.000887−0.001950
O110.0299070.0277970.022505−0.001843−0.0024710.001053
C120.0326250.0174200.0249420.0008070.004593−0.001037
C130.0271950.0174760.017983−0.0007260.000496−0.001429
C140.0311170.0224080.024507−0.002479−0.001739−0.003684
C150.0373200.0201800.027579−0.006433−0.002347−0.004962
F150.0461330.0252390.047625−0.011627−0.011007−0.008326
C160.0388100.0176260.025028−0.003222−0.001347−0.000411
C170.0357290.0202330.020763−0.001715−0.0032890.002305
F170.0452900.0272350.0320340.000137−0.0111650.008689
C180.0338990.0188600.020946−0.002359−0.0021480.000915
C210.0290860.0111460.018640−0.003423−0.0004970.000673
O210.0290500.0160040.027121−0.002958−0.000633−0.000759
C220.0330710.0093050.019673−0.002803−0.000383−0.000384
N200.0291540.0158280.020100−0.002225−0.001790−0.000181
C230.0475070.0158760.0231830.001348−0.0016790.005336
C310.0345590.0118590.021900−0.0030510.000249−0.000604
O310.0334400.0147770.035322−0.0013060.0047000.000939
C320.0330340.0094410.024850−0.0018930.0012530.000327
N300.0339710.0099510.029680−0.0035260.002765−0.003297
C330.0315480.0097240.024451−0.0000970.0030460.001227
C340.0378860.0139170.0308560.0045340.0052640.001459
C350.0445180.0176210.0310490.0039570.008168−0.001540
C360.0438450.0219610.024648−0.0013070.003621−0.001945
C370.0382320.0278620.0259250.0003660.0006090.000718
C380.0338310.0208100.0250270.0024010.0005920.000534
O400.0325810.0092960.023847−0.001985−0.0013160.001340
C400.0320580.0102770.019506−0.004369−0.0019070.001063
C410.0381110.0231880.023088−0.0041060.0017890.006886
C420.0350560.0131770.037404−0.000505−0.0027510.001670
C430.0390990.0221840.024111−0.003921−0.007487−0.003900
IS330.0957900.3198350.305352−0.018250−0.0220230.055111
IS340.1039290.3898000.421772−0.0305860.0278450.004137

Experimental details

(I)(PHENIX)
Crystal data
Chemical formulaC23H26F2N2O4?
Mr432.46?
Crystal system, space groupOrthorhombic, P212121Orthorhombic, P212121
Temperature (K)100?
a, b, c (Å)5.490 (5), 15.720 (15), 24.82 (2)5.49, 15.72, 24.82
α, β, γ (°)90, 90, 9090, 90, 90
V (Å3)2142 (4)?
Z4?
Radiation typeSynchrotron, λ = 0.70000 Å?, λ = ? Å
µ (mm−1)0.10?
Crystal size (mm)0.25 × 0.05 × 0.04 × ×
Data collection
DiffractometerMarresearch MAR300 CCD
diffractometer		?
Absorption correctionMulti-scan
(SCALEPACK; Otwinowski et al., 2003)		?
Tmin, Tmax0.974, 0.996?, ?
No. of measured, independent and
observed reflections		3216, 3216, 3157 [I > 2σ(I)]?, ?, ? (?)
Rint0.061?
(sin θ/λ)max (Å−1)0.694–
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.112, 1.10 ?, ?, ?
No. of reflections3216?
No. of parameters384?
No. of restraints0?
H-atom treatmentAll H-atom parameters refined–
Δρmax, Δρmin (e Å−3)0.35, −0.23?, ?

Computer programs: SERGUI, SERCAT APS beamline software, HKL-2000 (Otwinowski & Minor, 1997), SHELXD (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and pyMOL (DeLano, 2002).

Hydrogen-bond geometry (Å, º) for (I) top
D—H···AD—HH···AD···AD—H···A
N20—H201···O21i0.92 (4)2.03 (3)2.933 (3)165 (3)
Symmetry code: (i) x+1, y, z.
 

Acknowledgements

Richard Gildea and Luc Bourhis are thanked for their help with using smtbx tools. This work was funded in part with federal funds from the National Cancer Institute under contract No. NO1-CO-12400. The X-ray data were collected at the SERCAT 22ID beamline of the Advanced Photon Source, Argonne National Laboratory; use of the APS was supported by the US Department of Energy under contract No. W-31-109-Eng-38.

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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296
Volume 66| Part 12| December 2010| Pages o585-o588
doi:10.1107/S0108270110044136
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