An unusually short inter­molecular N—H...N hydrogen bond in crystals of the hemi-hydro­chloride salt of 1-exo-acetamido­pyrrolizidine

In the crystal, two AcAP mol­ecules related by a crystallographic twofold axis link to H⁺ and Cl⁻ ions lying on the rotation axis, thereby forming N—H...N and N—H...Cl...H—N hydrogen bonds. The first of these has an unusually short N...N separation of 2.616 (2) Å: refinement of different models against the present data set could not distinguish between a symmetrical hydrogen bond (H atom lying on the twofold axis and equidistant from the N atoms) or static or dynamic disorder models (i.e. N—H...N + N...H—N).

Key indicators

• Single-crystal X-ray study
• T = 90 K
• Mean [sigma](C-C) = 0.002 Å
• Disorder in main residue
• R factor = 0.037
• wR factor = 0.096
• Data-to-parameter ratio = 15.5

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       3.10 Report
PLAT303_ALERT_2_C Full Occupancy Atom H4N       with # Connections       2.00 Check
PLAT410_ALERT_2_C Short Intra H...H Contact  H1       ..H7'B     .       1.97 Ang.
                                                      x,y,z  =      1_555 Check
PLAT410_ALERT_2_C Short Intra H...H Contact  H3A      ..H5'B     .       1.95 Ang.
                                                      x,y,z  =      1_555 Check
PLAT771_ALERT_2_C Check   N-H Bond in CIF: N4       --H4N       ..       1.31 Ang.

Author Response: This is in intentional. The atoms in question take part in an exceptionally short N---H...N hydrogen bond that appears to be symmetric. The H atom electron density peak lies on a crystallographic 2-fold axis, which is exactly equidistant from N4 and its 2-fold related counterpart.

PLAT771_ALERT_2_C Check   N-H Bond in CIF: N4       --H4N       ..       1.31 Ang.

Author Response: This is in intentional. The atoms in question take part in an exceptionally short N---H...N hydrogen bond that appears to be symmetric. The H atom electron density peak lies on a crystallographic 2-fold axis, which is exactly equidistant from N4 and its 2-fold related counterpart.

PLAT776_ALERT_1_C Check   D-H Dist in CIF: N4       --H4N       ..       1.31 Ang.
PLAT906_ALERT_3_C Large K Value in the Analysis of Variance ......      2.228 Check
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600          4 Report
PLAT918_ALERT_3_C Reflection(s) with I(obs) much Smaller I(calc) .          1 Check

Alert level G
FORMU01_ALERT_1_G  There is a discrepancy between the atom counts in the
            _chemical_formula_sum and _chemical_formula_moiety. This is
            usually due to the moiety formula being in the wrong format.
            Atom count from _chemical_formula_sum:   C18 H33 Cl1 N4 O2
            Atom count from _chemical_formula_moiety:C27 H49 Cl1 N6 O3
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite          9 Note
PLAT003_ALERT_2_G Number of Uiso or Uij Restrained non-H Atoms ...          4 Report
PLAT171_ALERT_4_G The CIF-Embedded .res File Contains EADP Records          2 Report
PLAT175_ALERT_4_G The CIF-Embedded .res File Contains SAME Records          1 Report
PLAT178_ALERT_4_G The CIF-Embedded .res File Contains SIMU Records          2 Report
PLAT187_ALERT_4_G The CIF-Embedded .res File Contains RIGU Records          2 Report
PLAT301_ALERT_3_G Main Residue  Disorder ..............(Resd  1  )        33% Note
PLAT304_ALERT_4_G Non-Integer Number of Atoms in ..... (Resd  2  )       0.50 Check
PLAT720_ALERT_4_G Number of Unusual/Non-Standard Labels ..........          6 Note
PLAT779_ALERT_4_G Suspect or Irrelevant (Bond) Angle(s) in CIF . #         32 Check
              H4N  -N4   -H4N     1.555   1.555   1.555              0.00 Deg.
PLAT793_ALERT_4_G Model has Chirality at N4          (Centro SPGR)          S Verify
PLAT793_ALERT_4_G Model has Chirality at C1          (Centro SPGR)          S Verify
PLAT793_ALERT_4_G Model has Chirality at C8          (Centro SPGR)          R Verify
PLAT811_ALERT_5_G No ADDSYM Analysis: Too Many Excluded Atoms ....          ! Info
PLAT860_ALERT_3_G Number of Least-Squares Restraints .............         82 Note
PLAT910_ALERT_3_G Missing # of FCF Reflection(s) Below Theta(Min).          1 Note
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600          2 Note
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.          8 Info

   0 ALERT level A = Most likely a serious problem - resolve or explain
   0 ALERT level B = A potentially serious problem, consider carefully
  10 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  19 ALERT level G = General information/check it is not something unexpected

   2 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   9 ALERT type 2 Indicator that the structure model may be wrong or deficient
   6 ALERT type 3 Indicator that the structure quality may be low
  11 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

---

Computing details

Data collection: APEX3 (Bruker, 2016); cell refinement: APEX3 (Bruker, 2016); data reduction: APEX3 (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELX (Sheldrick, 2008), CIFFIX (Parkin, 2013) and PLATON (Spek, 2009).

(1R*, 8S)-2-acetamidooctahydropyrrolizin-4-ium chloride–N-[(1R, 8S)hexahydro-1H-pyrrolizin-2-yl)acetamide (1/1)

Crystal data

C9H17N2O^+·Cl^−·C9H16N2O	F(000) = 808
Mr = 372.93	Dx = 1.267 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 20.2125 (8) Å	Cell parameters from 9978 reflections
b = 9.6926 (4) Å	θ = 2.3–27.5°
c = 10.1458 (3) Å	µ = 0.22 mm^−1
β = 100.445 (1)°	T = 90 K
V = 1954.74 (13) Å^3	Plate, colourless
Z = 4	0.40 × 0.36 × 0.04 mm

Data collection

Bruker D8 Venture dual source diffractometer	2235 independent reflections
Radiation source: microsource	2096 reflections with I > 2σ(I)
Detector resolution: 7.41 pixels mm^-1	Rint = 0.032
φ and ω scans	θmax = 27.5°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	h = −26→26
Tmin = 0.885, Tmax = 0.988	k = −12→12
31903 measured reflections	l = −11→13

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: mixed
R[F^2 > 2σ(F^2)] = 0.037	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.096	w = 1/[σ^2(Fo^2) + (0.0375P)^2 + 2.4571P] where P = (Fo^2 + 2Fc^2)/3
S = 1.12	(Δ/σ)max < 0.001
2235 reflections	Δρmax = 0.67 e Å^−3
144 parameters	Δρmin = −0.22 e Å^−3
82 restraints	Extinction correction: SHELXL-2018/3 (Sheldrick 2018), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.005 (1)

Special details

Experimental. The crystal was mounted using polyisobutene oil on the tip of a fine glass fibre, which was fastened in a copper mounting pin with electrical solder. It was placed directly into the cold gas stream of a liquid-nitrogen based cryostat (Hope, 1994; Parkin & Hope, 1998).

Diffraction data were collected with the crystal at 90K, which is standard practice in this laboratory for the majority of flash-cooled crystals.

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.

Refinement. Refinement progress was checked using PLATON (Spek, 2009) and by an R-tensor (Parkin, 2000). The final model was further checked with the IUCr utility checkCIF.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
C1	0.63783 (6)	0.58377 (14)	0.26083 (13)	0.0182 (3)
H1	0.684523	0.622089	0.275591	0.022*
C2	0.60256 (7)	0.61745 (15)	0.11816 (14)	0.0229 (3)
H2A	0.632627	0.601397	0.052759	0.027*
H2B	0.561093	0.562062	0.092144	0.027*
C3	0.58652 (7)	0.76915 (15)	0.12835 (14)	0.0232 (3)
H3A	0.626574	0.826636	0.124182	0.028*
H3B	0.549608	0.797166	0.055229	0.028*
N4	0.56555 (6)	0.78256 (11)	0.26254 (11)	0.0184 (3)
H4N	0.500000	0.781 (3)	0.250000	0.056 (9)*
C5	0.5885 (2)	0.9121 (2)	0.3373 (3)	0.0249 (7)	0.897 (5)
H5A	0.554374	0.945176	0.388570	0.030*	0.897 (5)
H5B	0.597261	0.985720	0.275018	0.030*	0.897 (5)
C6	0.65299 (9)	0.87111 (17)	0.43106 (16)	0.0237 (4)	0.897 (5)
H6A	0.663640	0.935711	0.507555	0.028*	0.897 (5)
H6B	0.691530	0.867102	0.383296	0.028*	0.897 (5)
C7	0.63499 (12)	0.7276 (2)	0.4771 (2)	0.0209 (5)	0.897 (5)
H7A	0.675941	0.673734	0.512861	0.025*	0.897 (5)
H7B	0.606530	0.733983	0.546696	0.025*	0.897 (5)
C8	0.59630 (6)	0.66296 (13)	0.34850 (13)	0.0178 (3)	0.897 (5)
H8	0.559801	0.602145	0.370299	0.021*	0.897 (5)
C5'	0.595 (2)	0.9165 (19)	0.322 (2)	0.0249 (7)	0.103 (5)
H5'A	0.561158	0.991410	0.308580	0.030*	0.103 (5)
H5'B	0.634307	0.944647	0.282171	0.030*	0.103 (5)
C6'	0.6157 (9)	0.8793 (15)	0.4690 (15)	0.032 (3)	0.103 (5)
H6'A	0.576222	0.871718	0.513823	0.039*	0.103 (5)
H6'B	0.647840	0.947113	0.517395	0.039*	0.103 (5)
C7'	0.6489 (11)	0.739 (2)	0.458 (2)	0.030 (4)	0.103 (5)
H7'A	0.655595	0.689122	0.544614	0.036*	0.103 (5)
H7'B	0.692818	0.749314	0.428958	0.036*	0.103 (5)
C8'	0.59630 (6)	0.66296 (13)	0.34850 (13)	0.0178 (3)	0.103 (5)
H8'	0.563026	0.605013	0.385455	0.021*	0.103 (5)
N2	0.64091 (6)	0.43798 (12)	0.29157 (11)	0.0184 (3)
H2N	0.6002 (10)	0.390 (2)	0.2837 (19)	0.035 (5)*
C9	0.69841 (6)	0.36514 (14)	0.31606 (12)	0.0178 (3)
O1	0.75448 (5)	0.41694 (11)	0.32142 (11)	0.0260 (2)
C10	0.68897 (7)	0.21311 (14)	0.33748 (14)	0.0224 (3)
H10A	0.715908	0.185291	0.423611	0.034*
H10B	0.703494	0.160954	0.265024	0.034*
H10C	0.641361	0.194212	0.337727	0.034*
Cl1	0.500000	0.27309 (5)	0.250000	0.02141 (15)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0169 (6)	0.0170 (6)	0.0210 (6)	−0.0016 (5)	0.0044 (5)	0.0007 (5)
C2	0.0266 (7)	0.0247 (7)	0.0185 (6)	−0.0007 (5)	0.0071 (5)	0.0009 (5)
C3	0.0240 (7)	0.0244 (7)	0.0214 (7)	−0.0021 (5)	0.0041 (5)	0.0056 (5)
N4	0.0201 (5)	0.0139 (5)	0.0201 (6)	−0.0016 (4)	0.0006 (4)	0.0003 (4)
C5	0.0284 (13)	0.0147 (7)	0.0291 (10)	−0.0044 (6)	−0.0014 (9)	−0.0013 (6)
C6	0.0240 (9)	0.0220 (8)	0.0234 (8)	−0.0059 (6)	0.0001 (6)	−0.0025 (6)
C7	0.0237 (10)	0.0206 (8)	0.0174 (9)	0.0000 (7)	0.0015 (7)	−0.0004 (7)
C8	0.0189 (6)	0.0154 (6)	0.0187 (6)	0.0002 (5)	0.0020 (5)	0.0012 (5)
C5'	0.0284 (13)	0.0147 (7)	0.0291 (10)	−0.0044 (6)	−0.0014 (9)	−0.0013 (6)
C6'	0.033 (7)	0.028 (5)	0.033 (5)	−0.003 (5)	−0.001 (5)	−0.008 (4)
C7'	0.034 (8)	0.034 (6)	0.017 (7)	0.002 (6)	−0.003 (6)	−0.006 (5)
C8'	0.0189 (6)	0.0154 (6)	0.0187 (6)	0.0002 (5)	0.0020 (5)	0.0012 (5)
N2	0.0175 (5)	0.0155 (6)	0.0228 (6)	−0.0015 (4)	0.0049 (4)	−0.0005 (4)
C9	0.0200 (6)	0.0191 (6)	0.0142 (6)	−0.0007 (5)	0.0028 (5)	−0.0010 (5)
O1	0.0179 (5)	0.0247 (5)	0.0349 (6)	−0.0010 (4)	0.0029 (4)	0.0037 (4)
C10	0.0246 (7)	0.0178 (7)	0.0239 (7)	0.0004 (5)	0.0022 (5)	−0.0015 (5)
Cl1	0.0099 (2)	0.0177 (2)	0.0354 (3)	0.000	0.00096 (16)	0.000

Geometric parameters (Å, º)

C1—N2	1.4460 (17)	C6—H6B	0.9900
C1—C2	1.5284 (19)	C7—C8	1.529 (2)
C1—C8	1.5347 (18)	C7—H7A	0.9900
C1—C8'	1.5347 (18)	C7—H7B	0.9900
C1—H1	1.0000	C8—H8	1.0000
C2—C3	1.513 (2)	C5'—C6'	1.521 (18)
C2—H2A	0.9900	C5'—H5'A	0.9900
C2—H2B	0.9900	C5'—H5'B	0.9900
C3—N4	1.5032 (18)	C6'—C7'	1.528 (17)
C3—H3A	0.9900	C6'—H6'A	0.9900
C3—H3B	0.9900	C6'—H6'B	0.9900
N4—H4N	1.3080 (12)	C7'—C8'	1.576 (16)
N4—C5	1.497 (2)	C7'—H7'A	0.9900
N4—C5'	1.507 (17)	C7'—H7'B	0.9900
N4—C8	1.5146 (16)	C8'—H8'	1.0000
N4—C8'	1.5146 (16)	N2—C9	1.3439 (17)
N4—H4N	1.3080 (12)	N2—H2N	0.94 (2)
C5—C6	1.520 (4)	C9—O1	1.2317 (16)
C5—H5A	0.9900	C9—C10	1.5066 (19)
C5—H5B	0.9900	C10—H10A	0.9800
C6—C7	1.532 (3)	C10—H10B	0.9800
C6—H6A	0.9900	C10—H10C	0.9800
N2—C1—C2	114.05 (11)	C8—C7—C6	102.97 (16)
N2—C1—C8	111.75 (11)	C8—C7—H7A	111.2
C2—C1—C8	103.41 (11)	C6—C7—H7A	111.2
N2—C1—C8'	111.75 (11)	C8—C7—H7B	111.2
C2—C1—C8'	103.41 (11)	C6—C7—H7B	111.2
N2—C1—H1	109.1	H7A—C7—H7B	109.1
C2—C1—H1	109.1	N4—C8—C7	105.73 (12)
C8—C1—H1	109.1	N4—C8—C1	105.05 (10)
C3—C2—C1	102.22 (11)	C7—C8—C1	116.80 (13)
C3—C2—H2A	111.3	N4—C8—H8	109.7
C1—C2—H2A	111.3	C7—C8—H8	109.7
C3—C2—H2B	111.3	C1—C8—H8	109.7
C1—C2—H2B	111.3	N4—C5'—C6'	101.8 (12)
H2A—C2—H2B	109.2	N4—C5'—H5'A	111.4
N4—C3—C2	104.18 (11)	C6'—C5'—H5'A	111.4
N4—C3—H3A	110.9	N4—C5'—H5'B	111.4
C2—C3—H3A	110.9	C6'—C5'—H5'B	111.4
N4—C3—H3B	110.9	H5'A—C5'—H5'B	109.3
C2—C3—H3B	110.9	C5'—C6'—C7'	100.7 (16)
H3A—C3—H3B	108.9	C5'—C6'—H6'A	111.6
H4N—N4—C5	106.1 (12)	C7'—C6'—H6'A	111.6
H4N—N4—C3	110.96 (17)	C5'—C6'—H6'B	111.6
C5—N4—C3	114.78 (16)	C7'—C6'—H6'B	111.6
H4N—N4—C5'	112 (2)	H6'A—C6'—H6'B	109.4
C3—N4—C5'	106.2 (15)	C6'—C7'—C8'	102.6 (11)
H4N—N4—C8	110.4 (12)	C6'—C7'—H7'A	111.2
C5—N4—C8	107.04 (14)	C8'—C7'—H7'A	111.2
C3—N4—C8	107.55 (10)	C6'—C7'—H7'B	111.2
H4N—N4—C8'	110.4 (12)	C8'—C7'—H7'B	111.2
C3—N4—C8'	107.55 (10)	H7'A—C7'—H7'B	109.2
C5'—N4—C8'	109.8 (9)	N4—C8'—C1	105.05 (10)
H4N—N4—H4N	0 (3)	N4—C8'—C7'	101.6 (8)
C5—N4—H4N	106.1 (12)	C1—C8'—C7'	105.9 (9)
C3—N4—H4N	110.96 (17)	N4—C8'—H8'	114.3
C5'—N4—H4N	112 (2)	C1—C8'—H8'	114.3
C8—N4—H4N	110.4 (12)	C7'—C8'—H8'	114.3
C8'—N4—H4N	110.4 (12)	C9—N2—C1	123.73 (11)
N4—C5—C6	104.5 (2)	C9—N2—H2N	118.0 (12)
N4—C5—H5A	110.9	C1—N2—H2N	117.9 (12)
C6—C5—H5A	110.9	O1—C9—N2	123.50 (13)
N4—C5—H5B	110.9	O1—C9—C10	122.14 (13)
C6—C5—H5B	110.9	N2—C9—C10	114.37 (12)
H5A—C5—H5B	108.9	C9—C10—H10A	109.5
C5—C6—C7	101.78 (16)	C9—C10—H10B	109.5
C5—C6—H6A	111.4	H10A—C10—H10B	109.5
C7—C6—H6A	111.4	C9—C10—H10C	109.5
C5—C6—H6B	111.4	H10A—C10—H10C	109.5
C7—C6—H6B	111.4	H10B—C10—H10C	109.5
H6A—C6—H6B	109.3
N2—C1—C2—C3	162.24 (11)	N2—C1—C8—C7	93.71 (16)
C8—C1—C2—C3	40.67 (13)	C2—C1—C8—C7	−143.19 (14)
C8'—C1—C2—C3	40.67 (13)	H4N—N4—C5'—C6'	97 (2)
C1—C2—C3—N4	−39.46 (13)	C3—N4—C5'—C6'	−142 (2)
C2—C3—N4—H4N	−97.5 (15)	C8'—N4—C5'—C6'	−26 (3)
C2—C3—N4—C5	142.30 (19)	N4—C5'—C6'—C7'	45 (3)
C2—C3—N4—C5'	140.9 (15)	C5'—C6'—C7'—C8'	−47 (2)
C2—C3—N4—C8	23.32 (13)	H4N—N4—C8'—C1	123.3 (9)
C2—C3—N4—C8'	23.32 (13)	C3—N4—C8'—C1	2.12 (13)
H4N—N4—C5—C6	141.3 (8)	C5'—N4—C8'—C1	−113 (2)
C3—N4—C5—C6	−95.81 (19)	H4N—N4—C8'—C7'	−126.5 (13)
C8—N4—C5—C6	23.5 (3)	C3—N4—C8'—C7'	112.3 (10)
N4—C5—C6—C7	−39.9 (3)	C5'—N4—C8'—C7'	−3 (2)
C5—C6—C7—C8	40.9 (2)	N2—C1—C8'—N4	−149.53 (11)
H4N—N4—C8—C7	−112.6 (9)	C2—C1—C8'—N4	−26.43 (13)
C5—N4—C8—C7	2.4 (2)	N2—C1—C8'—C7'	103.4 (9)
C3—N4—C8—C7	126.23 (14)	C2—C1—C8'—C7'	−133.5 (9)
H4N—N4—C8—C1	123.3 (9)	C6'—C7'—C8'—N4	30.6 (18)
C5—N4—C8—C1	−121.70 (19)	C6'—C7'—C8'—C1	140.1 (14)
C3—N4—C8—C1	2.12 (13)	C2—C1—N2—C9	113.29 (14)
C6—C7—C8—N4	−26.97 (19)	C8—C1—N2—C9	−129.88 (13)
C6—C7—C8—C1	89.41 (17)	C8'—C1—N2—C9	−129.88 (13)
N2—C1—C8—N4	−149.53 (11)	C1—N2—C9—O1	3.8 (2)
C2—C1—C8—N4	−26.43 (13)	C1—N2—C9—C10	−176.47 (12)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4N···N4^i	1.31 (1)	1.31 (1)	2.616 (2)	178 (3)
N2—H2N···Cl1	0.94 (2)	2.29 (2)	3.2263 (11)	176.4 (16)

Symmetry code: (i) −x+1, y, −z+1/2.