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Crystal structure of N-{N-[N-(tert-but­­oxy­carbon­yl)-L-α-aspart­yl]-L-α-aspart­yl}-L-α-aspartic acid 14,24,34-tri­methyl ester 31-2-oxo-2-phenyl­ethyl ester {Boc-[Asp(OMe)]3-OPac}

CROSSMARK_Color_square_no_text.svg

aOsaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
*Correspondence e-mail: t.kato@gly.oups.ac.jp

Edited by H. Ishida, Okayama University, Japan (Received 8 March 2019; accepted 4 April 2019; online 9 April 2019)

In the title homotripeptide {Boc-[Asp(OMe)]3-OPac}, C28H37N3O13, all peptide bonds adopt an s-trans conformation with respect to the N—H and C=O groups. In the crystal, N—H⋯O hydrogen bonds result in an infinite parallel β-sheet structure running along the b-axis direction. The Boc protecting group at the N-terminus of the peptide is disordered over two sites with occupancy factors of 0.504 (5) and 0.496 (5).

1. Chemical context

In peptide stereochemistry, many studies have been performed in order to control the peptide's secondary structure. Among them, controlling helix handedness can greatly impact the design of some biological mol­ecules such as mol­ecular switches and the pharmaceutical lead like protein–protein inter­action inhibitors (de Zotti et al., 2014[De Zotti, M., Formaggio, F., Crisma, M., Peggion, C., Moretto, A. & Toniolo, C. (2014). J. Pept. Sci. 20, 307-322.]). Blout & Karlson (1958[Blout, E. R. & Karlson, R. H. (1958). J. Am. Chem. Soc. 80, 1259-1260.]) reported that the homopolymer of aspartic acid β-benzyl ester existed as a left-handed helix in solutions of halogenated hydro­carbones (CHCl3 and CCl2COOH), although early studies have clearly shown that a classical ordered α-helix structure in all-L peptides is right handed because of the absolute configuration of their α-amino acid building blocks. Subsequently, this research topic was expanded by many other groups, and numerous β-esters have been investigated (Toniolo et al., 1968[Toniolo, C., Falxa, M. L. & Goodman, M. (1968). Biopolymers, 6, 1579-1603.]). In this work, we focus on the homo-tripeptide of Asp(OMe) as a simple model of the homo-polypeptide because of the difficulties in collecting X-ray diffraction data for polypeptides.

[Scheme 1]

2. Structural commentary

Table 1[link] shows selected torsion angles for the title tripeptide. The mol­ecular structure of the tripeptide adopts an extended conformation of the backbone chain (Fig. 1[link]) with the φ- and ψ-torsion angles being φ1 = −122.49 (17)°, φ2 = −116.98 (16)°, φ3 = −84.60 (18)°, ψ1 = 86.49 (17)° and ψ2 = 112.58 (16)°, residing in the β region of the Ramachandran plot. All three consecutive peptide residues are in an s-trans conformation with the ω-torsion angles being ω0A = 169.2 (3)°, ω0B = −167.9 (2)°, ω1 = −168.62 (12)° and ω2 = −173.95 (13)°. The side chains of Asp(OMe), N2—C21—C23—C24 and N3—C31—C33—C34, adopt a g+ conformation [χ2 = −66.56 (19)° and χ3 = −57.72 (17)°], which is the most preferred conformation of aspartic acid (Chakrabarti & Pal, 2001[Chakrabarti, P. & Pal, D. (2001). Prog. Biophys. Mol. Biol. 76, 1-102.]), while the terminal side chain of Asp(OMe), N1—C11—C13—C14, adopts a t conformation [χ1 = 172.69 (15)°].

Table 1
Selected torsion angles (°)

Name Atoms Torsion angle
ω0A O4A—C5—N1—C11 169.2 (3)
ω0B O4B—C5—N1—C11 −167.9 (2)
φ1 C5—N1—C11—C12 −122.49 (17)
ψ1 N1—C11—C12—N2 86.49 (17)
ω1 C11—C12—N2—C21 −168.62 (12)
φ2 C12—N2—C21—C22 −116.98 (16)
ψ2 N2—C21—C22—N3 112.58 (16)
ω2 C21—C22—N3—C31 −173.95 (13)
φ3 C22—N3—C31—C32 −84.60 (18)
χ1 N1—C11—C13—C14 172.69 (15)
χ2 N2—C21—C23—C24 −66.56 (19)
χ3 N3—C31—C33—C34 −57.72 (17)
[Figure 1]
Figure 1
The mol­ecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. The minor component of the disordered group is drawn with dashed lines.

3. Supra­molecular features

In the crystal, all of the N atoms in the tripeptide are engaged in inter­molecular N—H⋯O hydrogen bonds [N1—H1⋯O5Ai, N1—H1⋯O5Bi, N2—H2⋯O12ii and N3—H3⋯O22i; Table 2[link]]. These hydrogen bonds and some C—H⋯O hydrogen bonds (C2A—H2A1⋯O4Aii, C13—H13⋯O5Ai, C13—H13⋯O5Bi, C31—H31⋯O35ii, C33—H33A⋯O41i and C41—H41A⋯O42ii; Table 2[link]) link the mol­ecules, forming an infinite parallel β-sheet structure along the b-axis direction (Fig. 2[link]). Other C—H⋯O hydrogen bonds [C15—H15B⋯O34iii, C25—H25B⋯O32iv and C46–H46⋯O34v; Table 2[link]] further link the β-sheets, forming a three-dimensional network (Fig. 3[link]).

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O5Ai 0.80 (3) 2.13 (3) 2.867 (11) 154 (2)
N1—H1⋯O5Bi 0.80 (3) 2.04 (3) 2.800 (10) 158 (2)
N2—H2⋯O12ii 0.89 (3) 2.22 (3) 3.066 (2) 159.5 (18)
N3—H3⋯O22i 0.85 (2) 2.16 (2) 2.995 (2) 170.1 (19)
C2A—H2A1⋯O4Aii 0.98 2.56 3.290 (12) 131
C13—H13B⋯O5Ai 0.99 2.48 3.300 (18) 140
C13—H13B⋯O5Bi 0.99 2.55 3.345 (17) 137
C15—H15B⋯O34iii 0.98 2.36 3.155 (2) 138
C25—H25B⋯O32iv 0.98 2.53 3.419 (2) 151
C31—H31⋯O35ii 1.00 2.34 3.319 (2) 164
C33—H33A⋯O41i 0.99 2.42 3.385 (2) 165
C41—H41A⋯O42ii 0.99 2.35 3.319 (2) 165
C46—H46⋯O34v 0.95 2.59 3.543 (3) 176
Symmetry codes: (i) x, y+1, z; (ii) x, y-1, z; (iii) [-x, y+{\script{1\over 2}}, -z]; (iv) [-x+1, y-{\script{1\over 2}}, -z+1]; (v) [-x+1, y+{\script{1\over 2}}, -z].
[Figure 2]
Figure 2
A packing diagram of the title compound, showing the infinite parallel β-sheet structure along the b-axis direction formed by the N—H⋯O and C—H⋯O hydrogen bonds (blue dashed lines). Only the major disorder component is shown. [Symmetry codes: (i) x, y + 1, z; (ii) x, y − 1, z.]
[Figure 3]
Figure 3
A packing diagram of the title compound viewed approximately along the b axis, showing the C—H⋯O hydrogen bonds between the β-sheets (blue dashed lines). Only the major disorder component is shown. [Symmetry codes: (iii) −x, y + [{1\over 2}], −z; (iv) −x + 1, y − [{1\over 2}], −z + 1; (v) −x + 1, y + [{1\over 2}], −z.]

4. Database survey

A search of the Cambridge Structural Database (Version 5.39, updated November 2017; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) for homo-dipeptides and tripeptides of Asp and Asp β-esters yielded zero hits. A search for dipeptides having an Asp(OMe) residue yielded two hits [DOBWIA (Fuganti et al., 1986[Fuganti, C., Grasselli, P., Malpezzi, L. & Casati, P. (1986). J. Org. Chem. 51, 1126-1128.]) and GABVEK (Mcharfi et al., 1986[Mcharfi, M., Aubry, A., Boussard, G. & Marraud, M. (1986). Eur. Biophys. J. 14, 43-51.])]. DOBWIA, an α-L-aspartyl-L-phenyl­alanine derivative, has an extended intra- and inter­molecular hydrogen-bonding network. GABVEK, an α-L-prolyl-L-aspartic acid derivative, shows a βI-turn conformation.

5. Synthesis and crystallization

The synthesis of the title homotripeptide, 6, was performed according to the scheme in Fig. 4[link].

[Figure 4]
Figure 4
Synthetic scheme for the title Asp(OMe) homo-tripeptide compound, 6.

Compound 1 was synthesized from L-aspartic acid according to a previously described method (Reddy et al., 2011[Reddy, C. R. & Latha, B. (2011). Tetrahedron Asymmetry, 22, 1849-1854.]; Ollivier et al., 2010[Ollivier, A., Sinibaldi, M. E., Toupet, L., Traïkia, M. & Canet, I. (2010). Tetrahedron Lett. 51, 4147-4149.]). Yield: 61.2% 1H NMR (400 MHz, CDCl3): δ 1.45 (s, 9H, Boc t-but­yl), 2.83–2.89 (m, 1H, Asp βH), 3.03–3.08 (m, 1H, Asp βH), 3.72 (s, 3H, Asp OCH3), 4.60–4.65 (m, 1H, Asp αH), 5.56 (d, J = 4.8 Hz, 1H, Asp NH).

Compound 2 was synthesized according to a slightly modified literature procedure (Wang et al., 1977[Wang, S. S., Gisin, B. F., Winter, D. P., Makofske, R., Kulesha, I. D., Tzougraki, C. & Meienhofer, J. (1977). J. Org. Chem. 42, 1286-1290.]). Compound 1 (7.05 g, 28.5 mmol) was dissolved in MeOH (20 mL) and 0.7 M aqueous Cs2CO3 solution (20 ml) was added. The mixture was evaporated to dryness and the residue was re-evaporated three times with EtOH. A mixture of the white solid cesium salt and phenacyl bromide (5.68 g, 28.5 mmol) in DMF (30 mL) was stirred for 15min, and the precipitated cesium bromide removed. The solution was evaporated to give the residue, which was diluted with ethyl acetate, washed with water, sat. aqueous NaHCO3, and dried over Na2SO4. The drying agent was filtered off and the filtrate evaporated under reduced pressure. Crystallization of the product from a mixture of ethyl acetate and hexane afforded colourless crystals. Yield 5.36 g (14.7 mmol, 51.5%). 1H NMR (400 MHz, CDCl3): δ 1.46 (s, 9H, Boc t-but­yl), 2.93–2.99 (m, 1H, Asp βH), 3.07–3.12 (m, 1H, Asp βH), 3.74 (s, 3H, Asp OCH3), 4.77–4.82 (m, 1H, Asp αH), 5.35–5.48 (m, 2H, Pac CH2), 5.59 (d, J = 8.8 Hz, Asp NH), 7.47–7.52 (m, 2H, Pac phen­yl), 7.60–7.64 (m, 1H, Pac phen­yl), 7.89–7.91 (m, 2H, Pac phen­yl).

Compound 3: Compound 2 (0.67 g, 2.72 mmol) was treated with 4.0 M HCl in dioxane for 60 min. The excess of HCl and solvent were evaporated and the residue was re-evaporated three times with MeOH, which was used for the next reaction without purification.

Compound 4: A solution of compound 1 (1.01 g, 2.72 mmol), compound 3 (2.72 mmol), 2-(1H-benzotriazol-1-yl)-1,1,3,3-tetra­methyl­uronium hexa­fluorido­phosphate (HBTU; 1.24 g, 3.26 mmol), 1,2,3-benzotriazol-1-ol monohydrate (HOBt; 0.44 g, 3.26 mmol) and iPr2NEt (1.11 ml, 6.52 mmol) in DMF was stirred at room temperature for 20 h. The solution was then evaporated, diluted with ethyl acetate, washed with sat. aqueous KHSO4 and sat. aqueous NaHCO3, and dried over Na2SO4. After evaporation of the solvent, the residue was purified by column chromatography on silica gel (50% EtOAc in n-hexa­ne). Crystallization of the product from a mixture of ethyl acetate and hexane (v:v = 1:1) afforded colourless crystals. Yield 0.70 g (1.42 mmol, 52.4%). 1H NMR (400 MHz, CDCl3): δ 1.45 (s, 9H, Boc t-but­yl), 2.71–3.03 (m, 2H, Asp βH), 2.95–3.13 (m, 2H, Asp βH), 3.70 (s, 3H, Asp OCH3), 3.75 (s, 3H, Asp OCH3), 4.58–4.60 (m, 1H, Asp αH), 5.03–5.08 (m, 1H, Asp αH), 5.35–5.47 (m, 2H, Pac CH2), 5.71 (d, J = 8.4 Hz, 1H, Asp NH), 7.47–7.51 (m, 2H, Pac phen­yl), 7.58 (d, J = 8.4 Hz, 1H, Asp NH), 7.60–7.64 (m, 2H, Pac phen­yl), 7.88–7.90 (m, 2H, Pac phen­yl).

Compound 5: Compound 4 (101.2 mg, 0.212 mmol) was treated with 4.0 M HCl in dioxane for 60 min. The excess of HCl and solvent were evaporated and the residue was re-evaporated three times with MeOH, which was used for the next reaction without purification.

Compound 6: A solution of compound 1 (57.7 mg, 0.233 mmol), compound 5 (0.212 mmol), 1-ethyl-3-(3-di­methyl­amino­prop­yl)carbodi­imide hydro­chloride (WSCHCl; 55.2 mg, 0.288 mmol), HOBt (37.1 mg, 0.275 mmol) and Et3N (71 µl, 0.509 mmol) in DMF was stirred at room temperature for 20 h. The solution was then evaporated, diluted with ethyl acetate, washed with sat. aqueous KHSO4 and sat. aqueous NaHCO3, and dried over Na2SO4. After evaporation of the solvent, the residue was purified by column chromatography on silica gel (66% EtOAc in n–hexa­ne). Crystallization of the product from a mixture of ethyl acetate and hexane (v:v = 1:1) afforded colourless crystals. Yield 77 mg (0.127 mmol, 59.9%). 1H NMR (400 MHz, CDCl3): δ 1.45 (s, 9H, Boc t-but­yl), 2.72–2.82 (m, 2H, Asp βH), 2.96–3.04 (m, 4H, Asp βH), 3.69 (s, 3H, Asp OCH3), 3.71 (s, 3H, Asp OCH3), 3.74 (s, 3H, Asp OCH3), 4.52–4.56 (m,1H, Asp αH), 4.83–4.88 (m, 1H, Asp αH), 5.03–5.08 (m, 1H, Asp aH), 5.33–5.46 (m, 2H, Pac CH2), 5.65 (d, J = 8.4Hz, 1H, Asp NH), 7.47–7.51 (m, 1H, Pac phen­yl), 7.60–7.64 (m, 3H, Pac phenyl, Asp NH), 7.87–7.89 (m, 2H, Pac phen­yl). Single crystals suitable for X-ray diffraction were obtained by slow evaporation from a solution of acetone/water (19:1 v/v) mixture.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. The Boc protecting group at the N-terminus of the peptide is disordered. The final occupancy ratio is 0.504 (5):0.496 (5). The C atoms of the disordered tert-butyl groups were refined with SIMU restraints and the C5—O5A and C5—O5B bonds were treated with DFIX restraints of 1.21 (1) Å. The N-bound H atoms were refined freely, while the other H atoms were placed in geometrically idealized positions (C—H = 0.95–1.00 Å) and refined as riding on their parent atoms, with Uiso(H) = 1.2Ueq(C) (or 1.5Ueq(C) for the methyl groups). The absolute configuration was known for the synthesized material.

Table 3
Experimental details

Crystal data
Chemical formula C28H37N3O13
Mr 623.60
Crystal system, space group Monoclinic, P21
Temperature (K) 93
a, b, c (Å) 17.7734 (2), 4.97864 (4), 18.7681 (2)
β (°) 114.2255 (14)
V3) 1514.49 (3)
Z 2
Radiation type Cu Kα
μ (mm−1) 0.93
Crystal size (mm) 0.41 × 0.14 × 0.04
 
Data collection
Diffractometer Rigaku Oxford Diffraction XtaLAB Pro: Kappa single
Absorption correction Multi-scan (CrysAlis PRO; Rigaku OD, 2015[Rigaku OD (2015). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.])
Tmin, Tmax 0.754, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 7024, 3952, 3832
Rint 0.018
(sin θ/λ)max−1) 0.625
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.026, 0.072, 0.77
No. of reflections 3952
No. of parameters 470
No. of restraints 21
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.17, −0.18
Absolute structure Flack x determined using 629 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter 0.06 (12)
Computer programs: CrysAlis PRO (Rigaku OD, 2015[Rigaku OD (2015). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.]), SHELXS (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2016/6 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2015); cell refinement: CrysAlis PRO (Rigaku OD, 2015); data reduction: CrysAlis PRO (Rigaku OD, 2015); program(s) used to solve structure: SHELXS (Sheldrick, 2008); program(s) used to refine structure: SHELXL2016/6 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: publCIF (Westrip, 2010).

N-{N-[N-(tert-butoxycarbonyl)-L-α-aspartyl]-L-α-aspartyl}-L-α-aspartic acid 14,24,34-trimethyl ester 31-2-oxo-2-phenylethyl ester top
Crystal data top
C28H37N3O13F(000) = 660
Mr = 623.60Dx = 1.367 Mg m3
Monoclinic, P21Cu Kα radiation, λ = 1.54184 Å
a = 17.7734 (2) ÅCell parameters from 5605 reflections
b = 4.97864 (4) Åθ = 4.8–74.0°
c = 18.7681 (2) ŵ = 0.93 mm1
β = 114.2255 (14)°T = 93 K
V = 1514.49 (3) Å3Plate, colorless
Z = 20.41 × 0.14 × 0.04 mm
Data collection top
Rigaku Oxford Diffraction XtaLAB Pro: Kappa single
diffractometer
3952 independent reflections
Radiation source: fine-focus sealed X-ray tube3832 reflections with I > 2σ(I)
Detector resolution: 5.811 pixels mm-1Rint = 0.018
ω scansθmax = 74.4°, θmin = 2.6°
Absorption correction: multi-scan
(CrysAlisPro; Rigaku OD, 2015)
h = 2121
Tmin = 0.754, Tmax = 1.000k = 63
7024 measured reflectionsl = 2323
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.026 w = 1/[σ2(Fo2) + (0.0741P)2 + 0.2745P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.072(Δ/σ)max < 0.001
S = 0.77Δρmax = 0.17 e Å3
3952 reflectionsΔρmin = 0.18 e Å3
470 parametersAbsolute structure: Flack x determined using 629 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
21 restraintsAbsolute structure parameter: 0.06 (12)
Special details top

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

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
C1A0.2144 (3)0.2721 (9)0.6848 (2)0.0345 (9)0.504 (5)
H1A10.2674690.3552410.6935930.052*0.504 (5)
H1A20.2209690.1575620.7294530.052*0.504 (5)
H1A30.1736860.4126110.6790500.052*0.504 (5)
C2A0.2520 (6)0.0962 (18)0.6151 (5)0.0266 (13)0.504 (5)
H2A10.2313990.2132640.5690730.040*0.504 (5)
H2A20.2673580.2055210.6624320.040*0.504 (5)
H2A30.3003860.0026350.6168860.040*0.504 (5)
C3A0.1022 (5)0.0283 (18)0.5951 (5)0.0263 (14)0.504 (5)
H3A10.0601780.1114950.5847500.039*0.504 (5)
H3A20.1068140.1327370.6409660.039*0.504 (5)
H3A30.0862300.1475140.5496650.039*0.504 (5)
C4A0.1848 (4)0.102 (2)0.6103 (5)0.0217 (15)0.504 (5)
O4A0.1746 (3)0.3070 (16)0.5505 (4)0.0261 (11)0.504 (5)
O5A0.1213 (9)0.008 (2)0.4475 (13)0.024 (2)0.504 (5)
C1B0.1534 (3)0.2751 (9)0.6701 (2)0.0328 (9)0.496 (5)
H1B10.1994360.4026290.6866950.049*0.496 (5)
H1B20.1590980.1581670.7140550.049*0.496 (5)
H1B30.1012230.3739080.6528700.049*0.496 (5)
C2B0.2381 (6)0.0274 (18)0.6260 (6)0.0288 (14)0.496 (5)
H2B10.2378620.1371670.5825330.043*0.496 (5)
H2B20.2499300.1416790.6718430.043*0.496 (5)
H2B30.2806820.1116250.6385120.043*0.496 (5)
C3B0.0818 (5)0.0926 (18)0.5758 (5)0.0254 (13)0.496 (5)
H3B10.0298140.0067750.5514140.038*0.496 (5)
H3B20.0822570.1928730.6209320.038*0.496 (5)
H3B30.0869290.2180990.5378380.038*0.496 (5)
C4B0.1541 (5)0.105 (3)0.6028 (6)0.0212 (15)0.496 (5)
O4B0.1433 (3)0.3082 (16)0.5416 (4)0.0220 (10)0.496 (5)
O5B0.1396 (9)0.001 (2)0.4505 (12)0.024 (2)0.496 (5)
C50.14313 (11)0.2319 (4)0.47256 (9)0.0202 (4)
N10.14230 (10)0.4450 (3)0.42909 (8)0.0207 (3)
H10.1496 (14)0.593 (6)0.4473 (13)0.025*
C110.12630 (9)0.4285 (4)0.34665 (8)0.0159 (3)
H110.1193070.2364910.3294810.019*
C120.20103 (9)0.5508 (4)0.33717 (8)0.0152 (3)
O120.20389 (7)0.7897 (3)0.32340 (7)0.0207 (3)
C130.04814 (9)0.5864 (4)0.29904 (9)0.0198 (4)
H13A0.0003620.4965140.3031030.024*
H13B0.0527960.7686420.3215380.024*
C140.03251 (9)0.6103 (4)0.21412 (9)0.0191 (3)
O140.05911 (8)0.4612 (3)0.17994 (7)0.0285 (3)
C150.03784 (11)0.8735 (5)0.09979 (10)0.0293 (4)
H15A0.0092891.0362280.0949240.044*
H15B0.0975700.8989980.0721560.044*
H15C0.0206540.7210490.0769390.044*
O150.01716 (7)0.8205 (3)0.18149 (7)0.0269 (3)
N20.26296 (8)0.3747 (3)0.34922 (8)0.0159 (3)
H20.2565 (12)0.199 (6)0.3536 (11)0.019*
C210.34413 (9)0.4635 (4)0.35689 (8)0.0156 (3)
H210.3446060.6639620.3538020.019*
C220.36114 (9)0.3452 (4)0.28995 (9)0.0160 (3)
O220.37002 (7)0.1028 (3)0.28428 (6)0.0206 (3)
C230.41063 (9)0.3731 (4)0.43516 (8)0.0185 (4)
H23A0.4067380.1765330.4409000.022*
H23B0.4658230.4136280.4367410.022*
C240.40034 (9)0.5149 (4)0.50166 (9)0.0187 (3)
O240.36527 (8)0.7236 (3)0.49676 (7)0.0276 (3)
O250.43715 (7)0.3764 (3)0.56861 (6)0.0243 (3)
C250.43003 (11)0.4982 (5)0.63560 (9)0.0289 (4)
H25A0.4504250.6833420.6415630.043*
H25B0.4628020.3953510.6827070.043*
H25C0.3720540.4983280.6278830.043*
N30.36442 (8)0.5253 (3)0.23773 (8)0.0165 (3)
H30.3610 (12)0.692 (5)0.2455 (12)0.020*
C310.37213 (9)0.4317 (4)0.16774 (8)0.0158 (3)
H310.3402290.2609200.1500680.019*
C320.46177 (10)0.3789 (4)0.18265 (8)0.0173 (3)
O320.52056 (7)0.5030 (3)0.22640 (6)0.0235 (3)
C330.33705 (10)0.6411 (4)0.10194 (9)0.0179 (3)
H33A0.3690660.8100660.1175880.021*
H33B0.3407080.5732290.0538840.021*
C340.24805 (10)0.6920 (4)0.08698 (9)0.0183 (3)
O340.19207 (7)0.5396 (3)0.05273 (7)0.0262 (3)
O350.24040 (7)0.9215 (3)0.11951 (7)0.0227 (3)
C350.15959 (11)0.9750 (5)0.11807 (12)0.0319 (4)
H35A0.1194010.9960610.0638450.048*
H35B0.1616731.1403870.1471460.048*
H35C0.1431000.8248070.1422500.048*
O410.46534 (7)0.1747 (3)0.13693 (7)0.0198 (3)
C410.54548 (10)0.1292 (4)0.13817 (10)0.0208 (4)
H41A0.5461040.0449840.1129600.025*
H41B0.5870620.1214320.1929140.025*
C420.56705 (10)0.3543 (4)0.09510 (9)0.0178 (3)
O420.51578 (7)0.5211 (3)0.05891 (6)0.0216 (3)
C430.65291 (10)0.3610 (4)0.09916 (8)0.0182 (3)
C440.67194 (10)0.5559 (4)0.05561 (9)0.0205 (4)
H440.6307730.6785840.0241580.025*
C450.71356 (10)0.1801 (4)0.14514 (9)0.0217 (4)
H450.7005570.0455720.1741900.026*
C460.75121 (11)0.5701 (4)0.05834 (9)0.0231 (4)
H460.7642120.7015510.0284460.028*
C470.79299 (11)0.1973 (4)0.14827 (10)0.0246 (4)
H470.8345440.0762500.1800230.030*
C480.81132 (10)0.3916 (5)0.10490 (10)0.0241 (4)
H480.8655730.4027780.1070590.029*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C1A0.068 (2)0.0176 (18)0.0219 (14)0.000 (2)0.0225 (18)0.0003 (14)
C2A0.029 (3)0.026 (4)0.026 (2)0.003 (3)0.0132 (15)0.003 (2)
C3A0.029 (4)0.026 (4)0.030 (4)0.001 (3)0.018 (3)0.008 (2)
C4A0.038 (4)0.015 (2)0.016 (2)0.001 (5)0.015 (4)0.003 (2)
O4A0.049 (3)0.0146 (17)0.0160 (18)0.003 (3)0.014 (3)0.0002 (14)
O5A0.036 (5)0.016 (3)0.025 (3)0.003 (2)0.018 (4)0.003 (2)
C1B0.067 (2)0.0182 (18)0.0208 (14)0.005 (2)0.0254 (17)0.0008 (14)
C2B0.029 (3)0.027 (4)0.029 (3)0.001 (3)0.0113 (17)0.007 (3)
C3B0.028 (3)0.021 (4)0.030 (4)0.005 (2)0.015 (3)0.006 (2)
C4B0.033 (4)0.015 (2)0.018 (2)0.001 (4)0.012 (3)0.0045 (19)
O4B0.040 (3)0.0113 (16)0.0166 (18)0.005 (3)0.013 (2)0.0007 (14)
O5B0.044 (6)0.011 (2)0.021 (2)0.005 (2)0.016 (4)0.0022 (17)
C50.0293 (8)0.0167 (9)0.0176 (7)0.0000 (8)0.0127 (6)0.0003 (7)
N10.0357 (8)0.0124 (8)0.0170 (6)0.0036 (7)0.0137 (6)0.0031 (6)
C110.0205 (7)0.0154 (9)0.0142 (6)0.0015 (7)0.0094 (6)0.0012 (6)
C120.0184 (7)0.0139 (9)0.0131 (6)0.0002 (7)0.0063 (5)0.0002 (6)
O120.0210 (6)0.0148 (7)0.0272 (6)0.0008 (5)0.0109 (5)0.0030 (5)
C130.0197 (7)0.0219 (9)0.0205 (7)0.0003 (7)0.0110 (6)0.0001 (7)
C140.0153 (7)0.0205 (9)0.0196 (7)0.0035 (7)0.0054 (6)0.0002 (7)
O140.0373 (7)0.0275 (8)0.0216 (5)0.0052 (6)0.0129 (5)0.0007 (6)
C150.0243 (8)0.0346 (12)0.0245 (8)0.0022 (9)0.0055 (6)0.0090 (9)
O150.0246 (6)0.0292 (8)0.0251 (6)0.0084 (6)0.0083 (5)0.0071 (6)
N20.0177 (6)0.0113 (8)0.0195 (6)0.0010 (6)0.0083 (5)0.0005 (6)
C210.0166 (7)0.0149 (9)0.0166 (7)0.0003 (6)0.0083 (5)0.0003 (7)
C220.0142 (7)0.0167 (10)0.0167 (7)0.0006 (7)0.0061 (6)0.0001 (7)
O220.0303 (6)0.0141 (7)0.0193 (5)0.0017 (5)0.0119 (5)0.0000 (5)
C230.0195 (7)0.0188 (9)0.0169 (7)0.0024 (7)0.0072 (6)0.0002 (7)
C240.0181 (7)0.0216 (9)0.0152 (7)0.0017 (8)0.0055 (5)0.0003 (7)
O240.0384 (7)0.0232 (8)0.0205 (5)0.0077 (6)0.0114 (5)0.0015 (6)
O250.0315 (6)0.0260 (7)0.0149 (5)0.0023 (6)0.0091 (4)0.0008 (5)
C250.0366 (9)0.0360 (12)0.0160 (7)0.0002 (10)0.0127 (7)0.0015 (8)
N30.0232 (6)0.0125 (8)0.0173 (6)0.0011 (6)0.0119 (5)0.0024 (6)
C310.0198 (7)0.0136 (9)0.0160 (6)0.0015 (6)0.0095 (5)0.0019 (6)
C320.0233 (7)0.0152 (9)0.0159 (6)0.0000 (7)0.0106 (6)0.0019 (7)
O320.0214 (5)0.0270 (7)0.0217 (5)0.0035 (6)0.0085 (4)0.0061 (6)
C330.0210 (7)0.0172 (9)0.0172 (7)0.0015 (7)0.0096 (6)0.0004 (7)
C340.0227 (8)0.0181 (9)0.0143 (6)0.0004 (7)0.0078 (6)0.0029 (7)
O340.0236 (6)0.0286 (8)0.0235 (5)0.0072 (6)0.0066 (5)0.0050 (6)
O350.0214 (6)0.0189 (7)0.0319 (6)0.0008 (5)0.0151 (5)0.0021 (6)
C350.0280 (9)0.0298 (12)0.0474 (10)0.0047 (9)0.0249 (8)0.0057 (10)
O410.0218 (5)0.0169 (7)0.0252 (5)0.0009 (5)0.0142 (4)0.0043 (5)
C410.0224 (8)0.0177 (10)0.0279 (8)0.0014 (7)0.0159 (7)0.0001 (7)
C420.0242 (7)0.0147 (9)0.0162 (6)0.0011 (7)0.0102 (6)0.0049 (7)
O420.0246 (6)0.0195 (7)0.0221 (5)0.0029 (5)0.0107 (4)0.0010 (5)
C430.0236 (8)0.0164 (9)0.0163 (6)0.0018 (7)0.0098 (6)0.0030 (7)
C440.0251 (8)0.0188 (10)0.0181 (7)0.0009 (7)0.0094 (6)0.0017 (7)
C450.0268 (8)0.0195 (10)0.0215 (7)0.0007 (8)0.0126 (6)0.0009 (7)
C460.0298 (8)0.0219 (10)0.0216 (7)0.0063 (8)0.0145 (7)0.0031 (7)
C470.0236 (8)0.0240 (10)0.0255 (8)0.0014 (8)0.0093 (6)0.0014 (8)
C480.0225 (8)0.0275 (10)0.0249 (8)0.0052 (8)0.0123 (6)0.0063 (8)
Geometric parameters (Å, º) top
C1A—C4A1.532 (11)N2—H20.89 (3)
C1A—H1A10.9800C21—C221.526 (2)
C1A—H1A20.9800C21—C231.527 (2)
C1A—H1A30.9800C21—H211.0000
C2A—C4A1.521 (10)C22—O221.227 (2)
C2A—H2A10.9800C22—N31.347 (2)
C2A—H2A20.9800C23—C241.509 (2)
C2A—H2A30.9800C23—H23A0.9900
C3A—C4A1.521 (10)C23—H23B0.9900
C3A—H3A10.9800C24—O241.196 (2)
C3A—H3A20.9800C24—O251.345 (2)
C3A—H3A30.9800O25—C251.447 (2)
C4A—O4A1.473 (13)C25—H25A0.9800
O4A—C51.387 (7)C25—H25B0.9800
O5A—C51.212 (9)C25—H25C0.9800
C1B—C4B1.527 (11)N3—C311.4522 (19)
C1B—H1B10.9800N3—H30.85 (3)
C1B—H1B20.9800C31—C321.523 (2)
C1B—H1B30.9800C31—C331.539 (2)
C2B—C4B1.523 (10)C31—H311.0000
C2B—H2B10.9800C32—O321.202 (2)
C2B—H2B20.9800C32—O411.348 (2)
C2B—H2B30.9800C33—C341.510 (2)
C3B—C4B1.529 (10)C33—H33A0.9900
C3B—H3B10.9800C33—H33B0.9900
C3B—H3B20.9800C34—O341.206 (2)
C3B—H3B30.9800C34—O351.328 (2)
C4B—O4B1.484 (13)O35—C351.450 (2)
O4B—C51.348 (7)C35—H35A0.9800
O5B—C51.216 (9)C35—H35B0.9800
C5—N11.335 (2)C35—H35C0.9800
N1—C111.4563 (18)O41—C411.4329 (19)
N1—H10.80 (3)C41—C421.520 (2)
C11—C131.526 (2)C41—H41A0.9900
C11—C121.536 (2)C41—H41B0.9900
C11—H111.0000C42—O421.214 (2)
C12—O121.222 (2)C42—C431.497 (2)
C12—N21.352 (2)C43—C441.397 (2)
C13—C141.506 (2)C43—C451.398 (2)
C13—H13A0.9900C44—C461.390 (2)
C13—H13B0.9900C44—H440.9500
C14—O141.198 (2)C45—C471.391 (2)
C14—O151.344 (2)C45—H450.9500
C15—O151.447 (2)C46—C481.389 (3)
C15—H15A0.9800C46—H460.9500
C15—H15B0.9800C47—C481.386 (3)
C15—H15C0.9800C47—H470.9500
N2—C211.4586 (19)C48—H480.9500
C4A—C1A—H1A1109.5C12—N2—C21121.62 (16)
C4A—C1A—H1A2109.5C12—N2—H2121.7 (14)
H1A1—C1A—H1A2109.5C21—N2—H2116.7 (13)
C4A—C1A—H1A3109.5N2—C21—C22108.90 (13)
H1A1—C1A—H1A3109.5N2—C21—C23110.44 (13)
H1A2—C1A—H1A3109.5C22—C21—C23109.98 (13)
C4A—C2A—H2A1109.5N2—C21—H21109.2
C4A—C2A—H2A2109.5C22—C21—H21109.2
H2A1—C2A—H2A2109.5C23—C21—H21109.2
C4A—C2A—H2A3109.5O22—C22—N3123.09 (15)
H2A1—C2A—H2A3109.5O22—C22—C21121.80 (15)
H2A2—C2A—H2A3109.5N3—C22—C21115.11 (16)
C4A—C3A—H3A1109.5C24—C23—C21110.43 (14)
C4A—C3A—H3A2109.5C24—C23—H23A109.6
H3A1—C3A—H3A2109.5C21—C23—H23A109.6
C4A—C3A—H3A3109.5C24—C23—H23B109.6
H3A1—C3A—H3A3109.5C21—C23—H23B109.6
H3A2—C3A—H3A3109.5H23A—C23—H23B108.1
O4A—C4A—C2A110.1 (7)O24—C24—O25123.78 (15)
O4A—C4A—C3A110.1 (6)O24—C24—C23125.39 (15)
C2A—C4A—C3A114.2 (9)O25—C24—C23110.82 (16)
O4A—C4A—C1A101.5 (8)C24—O25—C25114.48 (15)
C2A—C4A—C1A109.8 (6)O25—C25—H25A109.5
C3A—C4A—C1A110.5 (7)O25—C25—H25B109.5
C5—O4A—C4A119.1 (7)H25A—C25—H25B109.5
C4B—C1B—H1B1109.5O25—C25—H25C109.5
C4B—C1B—H1B2109.5H25A—C25—H25C109.5
H1B1—C1B—H1B2109.5H25B—C25—H25C109.5
C4B—C1B—H1B3109.5C22—N3—C31119.51 (15)
H1B1—C1B—H1B3109.5C22—N3—H3119.8 (14)
H1B2—C1B—H1B3109.5C31—N3—H3120.7 (14)
C4B—C2B—H2B1109.5N3—C31—C32111.65 (12)
C4B—C2B—H2B2109.5N3—C31—C33110.54 (14)
H2B1—C2B—H2B2109.5C32—C31—C33108.24 (12)
C4B—C2B—H2B3109.5N3—C31—H31108.8
H2B1—C2B—H2B3109.5C32—C31—H31108.8
H2B2—C2B—H2B3109.5C33—C31—H31108.8
C4B—C3B—H3B1109.5O32—C32—O41124.59 (15)
C4B—C3B—H3B2109.5O32—C32—C31125.98 (16)
H3B1—C3B—H3B2109.5O41—C32—C31109.40 (13)
C4B—C3B—H3B3109.5C34—C33—C31108.13 (12)
H3B1—C3B—H3B3109.5C34—C33—H33A110.1
H3B2—C3B—H3B3109.5C31—C33—H33A110.1
O4B—C4B—C2B108.5 (6)C34—C33—H33B110.1
O4B—C4B—C3B111.0 (7)C31—C33—H33B110.1
C2B—C4B—C3B114.2 (10)H33A—C33—H33B108.4
O4B—C4B—C1B102.7 (8)O34—C34—O35124.64 (15)
C2B—C4B—C1B110.1 (7)O34—C34—C33124.45 (17)
C3B—C4B—C1B109.8 (6)O35—C34—C33110.85 (14)
C5—O4B—C4B120.0 (7)C34—O35—C35115.91 (15)
O5A—C5—N1125.0 (11)O35—C35—H35A109.5
O5B—C5—N1124.0 (11)O35—C35—H35B109.5
O5B—C5—O4B124.9 (11)H35A—C35—H35B109.5
N1—C5—O4B111.0 (4)O35—C35—H35C109.5
O5A—C5—O4A125.8 (12)H35A—C35—H35C109.5
N1—C5—O4A109.2 (4)H35B—C35—H35C109.5
C5—N1—C11123.55 (15)C32—O41—C41114.52 (13)
C5—N1—H1120.9 (16)O41—C41—C42109.92 (14)
C11—N1—H1115.6 (16)O41—C41—H41A109.7
N1—C11—C13109.09 (13)C42—C41—H41A109.7
N1—C11—C12107.42 (12)O41—C41—H41B109.7
C13—C11—C12110.52 (13)C42—C41—H41B109.7
N1—C11—H11109.9H41A—C41—H41B108.2
C13—C11—H11109.9O42—C42—C43121.93 (16)
C12—C11—H11109.9O42—C42—C41120.44 (15)
O12—C12—N2124.40 (16)C43—C42—C41117.63 (15)
O12—C12—C11121.54 (15)C44—C43—C45119.89 (15)
N2—C12—C11113.98 (15)C44—C43—C42118.18 (15)
C14—C13—C11112.88 (13)C45—C43—C42121.93 (16)
C14—C13—H13A109.0C46—C44—C43119.93 (16)
C11—C13—H13A109.0C46—C44—H44120.0
C14—C13—H13B109.0C43—C44—H44120.0
C11—C13—H13B109.0C47—C45—C43119.89 (17)
H13A—C13—H13B107.8C47—C45—H45120.1
O14—C14—O15124.62 (15)C43—C45—H45120.1
O14—C14—C13125.16 (17)C48—C46—C44119.78 (17)
O15—C14—C13110.21 (15)C48—C46—H46120.1
O15—C15—H15A109.5C44—C46—H46120.1
O15—C15—H15B109.5C48—C47—C45119.80 (17)
H15A—C15—H15B109.5C48—C47—H47120.1
O15—C15—H15C109.5C45—C47—H47120.1
H15A—C15—H15C109.5C47—C48—C46120.71 (16)
H15B—C15—H15C109.5C47—C48—H48119.6
C14—O15—C15117.30 (14)C46—C48—H48119.6
C2A—C4A—O4A—C567.6 (7)C21—C23—C24—O2422.5 (2)
C3A—C4A—O4A—C559.1 (8)C21—C23—C24—O25158.28 (14)
C1A—C4A—O4A—C5176.2 (4)O24—C24—O25—C251.0 (2)
C2B—C4B—O4B—C561.7 (8)C23—C24—O25—C25179.82 (14)
C3B—C4B—O4B—C564.5 (8)O22—C22—N3—C315.2 (2)
C1B—C4B—O4B—C5178.2 (4)C21—C22—N3—C31173.95 (13)
C4B—O4B—C5—O5B11.0 (10)C22—N3—C31—C3284.60 (18)
C4B—O4B—C5—N1172.8 (4)C22—N3—C31—C33154.84 (14)
C4A—O4A—C5—O5A1.2 (10)N3—C31—C32—O3234.3 (2)
C4A—O4A—C5—N1177.4 (4)C33—C31—C32—O3287.64 (19)
O5A—C5—N1—C119.4 (9)N3—C31—C32—O41147.76 (14)
O5B—C5—N1—C118.3 (9)C33—C31—C32—O4190.35 (16)
O4B—C5—N1—C11167.9 (2)N3—C31—C33—C3457.72 (17)
O4A—C5—N1—C11169.2 (3)C32—C31—C33—C34179.70 (14)
C5—N1—C11—C13117.68 (19)C31—C33—C34—O3475.17 (19)
C5—N1—C11—C12122.49 (17)C31—C33—C34—O35102.17 (16)
N1—C11—C12—O1290.42 (18)O34—C34—O35—C355.2 (2)
C13—C11—C12—O1228.5 (2)C33—C34—O35—C35172.12 (14)
N1—C11—C12—N286.49 (17)O32—C32—O41—C415.8 (2)
C13—C11—C12—N2154.60 (13)C31—C32—O41—C41172.21 (13)
N1—C11—C13—C14172.69 (15)C32—O41—C41—C4271.55 (17)
C12—C11—C13—C1454.80 (19)O41—C41—C42—O427.9 (2)
C11—C13—C14—O1422.9 (3)O41—C41—C42—C43172.15 (13)
C11—C13—C14—O15158.40 (14)O42—C42—C43—C444.2 (2)
O14—C14—O15—C151.8 (3)C41—C42—C43—C44175.78 (15)
C13—C14—O15—C15179.47 (15)O42—C42—C43—C45175.55 (16)
O12—C12—N2—C218.2 (2)C41—C42—C43—C454.5 (2)
C11—C12—N2—C21168.62 (12)C45—C43—C44—C460.3 (3)
C12—N2—C21—C22116.98 (16)C42—C43—C44—C46179.46 (15)
C12—N2—C21—C23122.15 (16)C44—C43—C45—C471.0 (3)
N2—C21—C22—O2266.5 (2)C42—C43—C45—C47178.75 (16)
C23—C21—C22—O2254.6 (2)C43—C44—C46—C480.5 (3)
N2—C21—C22—N3112.58 (16)C43—C45—C47—C480.9 (3)
C23—C21—C22—N3126.27 (15)C45—C47—C48—C460.1 (3)
N2—C21—C23—C2466.56 (19)C44—C46—C48—C470.6 (3)
C22—C21—C23—C24173.22 (14)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O5Ai0.80 (3)2.13 (3)2.867 (11)154 (2)
N1—H1···O5Bi0.80 (3)2.04 (3)2.800 (10)158 (2)
N2—H2···O12ii0.89 (3)2.22 (3)3.066 (2)159.5 (18)
N3—H3···O22i0.85 (2)2.16 (2)2.995 (2)170.1 (19)
C2A—H2A1···O4Aii0.982.563.290 (12)131
C13—H13B···O5Ai0.992.483.300 (18)140
C13—H13B···O5Bi0.992.553.345 (17)137
C15—H15B···O34iii0.982.363.155 (2)138
C25—H25B···O32iv0.982.533.419 (2)151
C31—H31···O35ii1.002.343.319 (2)164
C33—H33A···O41i0.992.423.385 (2)165
C41—H41A···O42ii0.992.353.319 (2)165
C46—H46···O34v0.952.593.543 (3)176
Symmetry codes: (i) x, y+1, z; (ii) x, y1, z; (iii) x, y+1/2, z; (iv) x+1, y1/2, z+1; (v) x+1, y+1/2, z.
Selected torsion angles (°) top
NameAtomsTorsion angle
ω0AO4A—C5—N1—C11169.2 (3)
ω0BO4B—C5—N1—C11-167.9 (2)
φ1C5—N1—C11—C12-122.49 (17)
ψ1N1—C11—C12—N286.49 (17)
ω1C11—C12—N2—C21-168.62 (12)
φ2C12—N2—C21—C22-116.98 (16)
ψ2N2—C21—C22—N3112.58 (16)
ω2C21—C22—N3—C31-173.95 (13)
φ3C22—N3—C31—C32-84.60 (18)
χ1N1—C11—C13—C14172.69 (15)
χ2N2—C21—C23—C24-66.56 (19)
χ3N3—C31—C33—C34-57.72 (17)
 

Acknowledgements

This work was performed in part under the Cooperative Research Program of the Institute for Protein Research, Osaka University (CR-18–05).

Funding information

Funding for this research was provided by: Grant-in-Aid for Research Activity Start-up (grant No. JP17H07269).

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