Crystal and geometry-optimized structure of an anthracene-based Diels–Alder adduct

Hillman, Z.E.; Tanski, J.M.; Roberts, A.

doi:10.1107/S2053229620008128

Crystal and geometry-optimized structure of an anthracene-based Diels–Alder adduct

Z. E. Hillman, J. M. Tanski and A. Roberts

Computational calculations of an anthracene-based Diels–Alder adduct, namely, 17-ethyl-1-hydroxymethyl-17-azapentacyclo[6.6.5.0^2,7.0^9,14.0^15,19]nonadeca-2,4,6,9,11,13-hexaene-16,18-dione, C₂₁H₁₉NO₃, predicting density functional theory (DFT) optimized geometries in the gas phase are compared in terms of accuracy relative to the solid-state crystal structure and computational cost. Crystal structure determination and Hirshfeld surface analysis of the racemic product reveal that the molecules are linked by O—H

O=C hydrogen bonds between the hydroxy and carbonyl groups, accounting for 9.5% of the intermolecular contacts, while H

H contacts represent 56.9% of the total. Boltzmann population analysis of computed relative rotamer abundances in the gas phase are based on lower-level geometry optimization and thermochemical corrections coupled with higher-level electronic energy calculations using the B2PLYP double-hybrid functional. As expected, the choice of density functional has a greater effect than the basis set on accuracy for all levels of theory. For any given functional, increasing the basis set size did not always correlate with increasingly accurate structures. The hybrid functional B3LYP without dispersion correction routinely gave the closest approximations to the crystal structure where the B3LYP/aug-cc-pVDZ combination afforded the best structure (r.m.s. deviation = 0.1314 Å). However, the B3LYP/6-31+G(d,p) level of theory represents the best compromise between accuracy (r.m.s. deviation = 0.1388 Å) and cost as it yielded appreciably accurate results in a fraction of the time compared to other method combinations.

Keywords: anthracene; Diels-Alder; computational chemistry; DFT; crystal structure; Boltzmann population analysis.

Read article Similar articles

Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229620008128/qf3039sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229620008128/qf3039Isup2.hkl Contains datablock I
	Portable Document Format (PDF) file https://doi.org/10.1107/S2053229620008128/qf3039sup3.pdf Experimental spectroscopic determinations, X-Ray diffraction data, and computational results
	Chemical Markup Language (CML) file https://doi.org/10.1107/S2053229620008128/qf3039Isup4.cml Supplementary material

CCDC reference: 1583410

Computing details top

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: SHELXTL2014 (Sheldrick, 2008); software used to prepare material for publication: SHELXTL2014 (Sheldrick, 2008).

17-Ethyl-1-hydroxymethyl-17-azapentacyclo[6.6.5.0^2,7.0^9,14.0^15,19]nonadeca-2,4,6,9,11,13-hexaene-16,18-dione top

Crystal data top

C₂₁H₁₉NO₃	F(000) = 704
M_r = 333.37	D_x = 1.337 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 12.2110 (13) Å	Cell parameters from 9901 reflections
b = 8.1447 (9) Å	θ = 2.8–31.5°
c = 17.6634 (19) Å	µ = 0.09 mm⁻¹
β = 109.430 (2)°	T = 125 K
V = 1656.7 (3) Å³	Block, colourless
Z = 4	0.33 × 0.26 × 0.20 mm

Data collection top

Bruker APEXII CCD diffractometer	5486 independent reflections
Radiation source: fine-focus sealed tube	4784 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.028
Detector resolution: 8.3333 pixels mm^-1	θ_max = 31.5°, θ_min = 1.8°
φ and ω scans	h = −17→17
Absorption correction: multi-scan (SADABS; Bruker, 2013)	k = −11→11
T_min = 0.90, T_max = 0.98	l = −25→25
36543 measured reflections

Refinement top

Refinement on F²	1 restraint
Least-squares matrix: full	Hydrogen site location: mixed
R[F² > 2σ(F²)] = 0.039	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.110	w = 1/[σ²(F_o²) + (0.0633P)² + 0.4753P] where P = (F_o² + 2F_c²)/3
S = 1.02	(Δ/σ)_max = 0.001
5486 reflections	Δρ_max = 0.50 e Å⁻³
230 parameters	Δρ_min = −0.22 e Å⁻³

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

	x	y	z	U_iso*/U_eq
O1	0.73973 (6)	0.96692 (8)	0.50764 (4)	0.02254 (15)
O2	0.85332 (6)	0.43164 (8)	0.53871 (4)	0.01947 (14)
O3	0.64094 (6)	0.20767 (8)	0.58591 (4)	0.01919 (14)
H3	0.6757 (11)	0.1545 (16)	0.5608 (8)	0.023*
N1	0.81304 (6)	0.70584 (9)	0.51418 (4)	0.01427 (14)
C1	0.68346 (7)	0.48699 (9)	0.63505 (5)	0.01212 (14)
C2	0.56498 (7)	0.52050 (10)	0.64336 (5)	0.01331 (14)
C3	0.49221 (7)	0.40476 (11)	0.66004 (5)	0.01628 (16)
H3B	0.515	0.2928	0.6681	0.02*
C4	0.38528 (8)	0.45515 (12)	0.66472 (5)	0.01995 (17)
H4A	0.3354	0.377	0.6764	0.024*
C5	0.35126 (8)	0.61850 (13)	0.65242 (6)	0.02073 (18)
H5A	0.2777	0.6508	0.6547	0.025*
C6	0.42446 (7)	0.73570 (11)	0.63676 (5)	0.01791 (16)
H6A	0.4014	0.8475	0.6288	0.021*
C7	0.53159 (7)	0.68625 (10)	0.63305 (5)	0.01386 (15)
C8	0.62088 (7)	0.79749 (10)	0.61719 (5)	0.01353 (14)
H8A	0.5972	0.9156	0.613	0.016*
C9	0.73581 (7)	0.76794 (10)	0.68294 (5)	0.01299 (14)
C10	0.80741 (8)	0.88879 (10)	0.72961 (5)	0.01651 (16)
H10A	0.7859	1.0012	0.7212	0.02*
C11	0.91105 (8)	0.84398 (12)	0.78889 (5)	0.01926 (17)
H11A	0.9597	0.9259	0.8215	0.023*
C12	0.94309 (8)	0.67986 (12)	0.80034 (5)	0.01901 (17)
H12A	1.0135	0.6501	0.841	0.023*
C13	0.87269 (7)	0.55800 (11)	0.75254 (5)	0.01583 (15)
H13A	0.8954	0.446	0.7602	0.019*
C14	0.76898 (7)	0.60215 (10)	0.69361 (5)	0.01276 (14)
C15	0.67343 (7)	0.55010 (9)	0.54881 (5)	0.01195 (14)
H15A	0.6158	0.4816	0.5073	0.014*
C16	0.63540 (7)	0.73176 (10)	0.53816 (5)	0.01289 (14)
H16A	0.5606	0.743	0.4927	0.015*
C17	0.73168 (7)	0.81973 (10)	0.51840 (5)	0.01469 (15)
C18	0.78911 (7)	0.54773 (10)	0.53426 (5)	0.01320 (14)
C19	0.91711 (8)	0.74664 (11)	0.49436 (6)	0.01882 (17)
H19A	0.899	0.8381	0.4552	0.023*
H19B	0.9399	0.6504	0.4687	0.023*
C20	1.01784 (9)	0.79573 (14)	0.56769 (7)	0.0291 (2)
H20A	1.0848	0.8246	0.5515	0.044*
H20B	1.0384	0.7038	0.6056	0.044*
H20C	0.9955	0.8906	0.5934	0.044*
C21	0.71934 (7)	0.30681 (10)	0.64652 (5)	0.01569 (15)
H21A	0.7988	0.2945	0.6442	0.019*
H21B	0.7202	0.2694	0.7	0.019*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0308 (4)	0.0125 (3)	0.0299 (4)	0.0021 (2)	0.0174 (3)	0.0041 (2)
O2	0.0193 (3)	0.0163 (3)	0.0251 (3)	0.0056 (2)	0.0104 (2)	0.0001 (2)
O3	0.0195 (3)	0.0121 (3)	0.0267 (3)	−0.0006 (2)	0.0085 (2)	−0.0046 (2)
N1	0.0149 (3)	0.0134 (3)	0.0166 (3)	0.0003 (2)	0.0081 (2)	−0.0003 (2)
C1	0.0122 (3)	0.0099 (3)	0.0142 (3)	0.0011 (2)	0.0044 (3)	0.0006 (2)
C2	0.0126 (3)	0.0144 (3)	0.0132 (3)	0.0009 (3)	0.0047 (3)	0.0006 (3)
C3	0.0170 (4)	0.0173 (4)	0.0157 (3)	−0.0015 (3)	0.0069 (3)	0.0012 (3)
C4	0.0175 (4)	0.0266 (4)	0.0183 (4)	−0.0036 (3)	0.0093 (3)	−0.0004 (3)
C5	0.0151 (4)	0.0297 (5)	0.0197 (4)	0.0017 (3)	0.0090 (3)	−0.0020 (3)
C6	0.0159 (4)	0.0211 (4)	0.0178 (4)	0.0049 (3)	0.0070 (3)	−0.0003 (3)
C7	0.0140 (3)	0.0145 (3)	0.0139 (3)	0.0018 (3)	0.0056 (3)	−0.0001 (3)
C8	0.0146 (3)	0.0110 (3)	0.0161 (3)	0.0025 (3)	0.0066 (3)	0.0003 (3)
C9	0.0142 (3)	0.0121 (3)	0.0138 (3)	0.0004 (3)	0.0063 (3)	−0.0004 (3)
C10	0.0202 (4)	0.0140 (3)	0.0177 (4)	−0.0029 (3)	0.0094 (3)	−0.0025 (3)
C11	0.0189 (4)	0.0216 (4)	0.0179 (4)	−0.0064 (3)	0.0071 (3)	−0.0041 (3)
C12	0.0150 (4)	0.0246 (4)	0.0162 (4)	−0.0029 (3)	0.0036 (3)	0.0005 (3)
C13	0.0144 (3)	0.0176 (4)	0.0152 (3)	0.0008 (3)	0.0046 (3)	0.0021 (3)
C14	0.0128 (3)	0.0127 (3)	0.0134 (3)	0.0001 (3)	0.0053 (3)	0.0002 (3)
C15	0.0120 (3)	0.0105 (3)	0.0137 (3)	0.0016 (2)	0.0046 (3)	0.0002 (2)
C16	0.0136 (3)	0.0114 (3)	0.0144 (3)	0.0025 (3)	0.0057 (3)	0.0014 (3)
C17	0.0176 (4)	0.0132 (3)	0.0145 (3)	0.0018 (3)	0.0070 (3)	0.0009 (3)
C18	0.0141 (3)	0.0128 (3)	0.0130 (3)	0.0005 (3)	0.0049 (3)	−0.0011 (3)
C19	0.0187 (4)	0.0198 (4)	0.0222 (4)	−0.0020 (3)	0.0125 (3)	−0.0009 (3)
C20	0.0205 (4)	0.0314 (5)	0.0344 (5)	−0.0062 (4)	0.0078 (4)	−0.0059 (4)
C21	0.0162 (4)	0.0106 (3)	0.0194 (4)	0.0015 (3)	0.0049 (3)	0.0012 (3)

Geometric parameters (Å, º) top

O1—C17	1.2229 (10)	C8—H8A	1.0
O2—C18	1.2140 (10)	C9—C10	1.3904 (11)
O3—C21	1.4257 (10)	C9—C14	1.4044 (11)
O3—H3	0.830 (12)	C10—C11	1.3963 (13)
N1—C17	1.3792 (10)	C10—H10A	0.95
N1—C18	1.3923 (11)	C11—C12	1.3886 (13)
N1—C19	1.4643 (11)	C11—H11A	0.95
C1—C14	1.5237 (11)	C12—C13	1.3979 (12)
C1—C21	1.5256 (11)	C12—H12A	0.95
C1—C2	1.5266 (11)	C13—C14	1.3926 (11)
C1—C15	1.5734 (11)	C13—H13A	0.95
C2—C3	1.3926 (11)	C15—C18	1.5177 (11)
C2—C7	1.4044 (11)	C15—C16	1.5434 (11)
C3—C4	1.3971 (12)	C15—H15A	1.0
C3—H3B	0.95	C16—C17	1.5134 (11)
C4—C5	1.3891 (14)	C16—H16A	1.0
C4—H4A	0.95	C19—C20	1.5135 (14)
C5—C6	1.3969 (13)	C19—H19A	0.99
C5—H5A	0.95	C19—H19B	0.99
C6—C7	1.3910 (11)	C20—H20A	0.98
C6—H6A	0.95	C20—H20B	0.98
C7—C8	1.5137 (11)	C20—H20C	0.98
C8—C9	1.5139 (11)	C21—H21A	0.99
C8—C16	1.5592 (11)	C21—H21B	0.99

C21—O3—H3	111.2 (9)	C11—C12—H12A	119.7
C17—N1—C18	113.10 (7)	C13—C12—H12A	119.7
C17—N1—C19	123.94 (7)	C14—C13—C12	119.45 (8)
C18—N1—C19	122.90 (7)	C14—C13—H13A	120.3
C14—C1—C21	113.59 (7)	C12—C13—H13A	120.3
C14—C1—C2	106.38 (6)	C13—C14—C9	119.91 (7)
C21—C1—C2	113.50 (7)	C13—C14—C1	126.58 (7)
C14—C1—C15	105.74 (6)	C9—C14—C1	113.50 (7)
C21—C1—C15	111.67 (6)	C18—C15—C16	104.53 (6)
C2—C1—C15	105.29 (6)	C18—C15—C1	112.50 (6)
C3—C2—C7	120.00 (7)	C16—C15—C1	110.76 (6)
C3—C2—C1	126.24 (7)	C18—C15—H15A	109.6
C7—C2—C1	113.76 (7)	C16—C15—H15A	109.6
C2—C3—C4	119.23 (8)	C1—C15—H15A	109.6
C2—C3—H3B	120.4	C17—C16—C15	104.87 (6)
C4—C3—H3B	120.4	C17—C16—C8	111.86 (7)
C5—C4—C3	120.58 (8)	C15—C16—C8	109.83 (6)
C5—C4—H4A	119.7	C17—C16—H16A	110.1
C3—C4—H4A	119.7	C15—C16—H16A	110.1
C4—C5—C6	120.51 (8)	C8—C16—H16A	110.1
C4—C5—H5A	119.7	O1—C17—N1	123.67 (8)
C6—C5—H5A	119.7	O1—C17—C16	127.49 (8)
C7—C6—C5	119.03 (8)	N1—C17—C16	108.84 (7)
C7—C6—H6A	120.5	O2—C18—N1	123.44 (8)
C5—C6—H6A	120.5	O2—C18—C15	128.05 (8)
C6—C7—C2	120.61 (8)	N1—C18—C15	108.50 (6)
C6—C7—C8	125.59 (8)	N1—C19—C20	112.22 (8)
C2—C7—C8	113.79 (7)	N1—C19—H19A	109.2
C7—C8—C9	107.68 (7)	C20—C19—H19A	109.2
C7—C8—C16	105.28 (6)	N1—C19—H19B	109.2
C9—C8—C16	106.25 (6)	C20—C19—H19B	109.2
C7—C8—H8A	112.4	H19A—C19—H19B	107.9
C9—C8—H8A	112.4	C19—C20—H20A	109.5
C16—C8—H8A	112.4	C19—C20—H20B	109.5
C10—C9—C14	120.31 (8)	H20A—C20—H20B	109.5
C10—C9—C8	125.58 (7)	C19—C20—H20C	109.5
C14—C9—C8	114.09 (7)	H20A—C20—H20C	109.5
C9—C10—C11	119.60 (8)	H20B—C20—H20C	109.5
C9—C10—H10A	120.2	O3—C21—C1	110.71 (7)
C11—C10—H10A	120.2	O3—C21—H21A	109.5
C12—C11—C10	120.13 (8)	C1—C21—H21A	109.5
C12—C11—H11A	119.9	O3—C21—H21B	109.5
C10—C11—H11A	119.9	C1—C21—H21B	109.5
C11—C12—C13	120.58 (8)	H21A—C21—H21B	108.1

C14—C1—C2—C3	−125.36 (8)	C21—C1—C14—C9	179.99 (7)
C21—C1—C2—C3	0.28 (12)	C2—C1—C14—C9	−54.43 (9)
C15—C1—C2—C3	122.71 (8)	C15—C1—C14—C9	57.19 (8)
C14—C1—C2—C7	54.22 (9)	C14—C1—C15—C18	59.80 (8)
C21—C1—C2—C7	179.86 (7)	C21—C1—C15—C18	−64.22 (8)
C15—C1—C2—C7	−57.71 (8)	C2—C1—C15—C18	172.18 (6)
C7—C2—C3—C4	1.27 (12)	C14—C1—C15—C16	−56.78 (8)
C1—C2—C3—C4	−179.18 (8)	C21—C1—C15—C16	179.21 (6)
C2—C3—C4—C5	0.40 (13)	C2—C1—C15—C16	55.60 (8)
C3—C4—C5—C6	−1.29 (14)	C18—C15—C16—C17	−0.01 (8)
C4—C5—C6—C7	0.48 (13)	C1—C15—C16—C17	121.39 (7)
C5—C6—C7—C2	1.20 (13)	C18—C15—C16—C8	−120.36 (7)
C5—C6—C7—C8	−179.64 (8)	C1—C15—C16—C8	1.04 (9)
C3—C2—C7—C6	−2.09 (12)	C7—C8—C16—C17	−174.10 (6)
C1—C2—C7—C6	178.31 (7)	C9—C8—C16—C17	−60.04 (8)
C3—C2—C7—C8	178.66 (7)	C7—C8—C16—C15	−58.08 (8)
C1—C2—C7—C8	−0.94 (10)	C9—C8—C16—C15	55.97 (8)
C6—C7—C8—C9	128.23 (8)	C18—N1—C17—O1	175.69 (8)
C2—C7—C8—C9	−52.57 (9)	C19—N1—C17—O1	−1.61 (13)
C6—C7—C8—C16	−118.72 (9)	C18—N1—C17—C16	−4.18 (9)
C2—C7—C8—C16	60.49 (8)	C19—N1—C17—C16	178.52 (7)
C7—C8—C9—C10	−128.93 (8)	C15—C16—C17—O1	−177.46 (9)
C16—C8—C9—C10	118.67 (8)	C8—C16—C17—O1	−58.47 (11)
C7—C8—C9—C14	52.38 (9)	C15—C16—C17—N1	2.39 (8)
C16—C8—C9—C14	−60.03 (8)	C8—C16—C17—N1	121.39 (7)
C14—C9—C10—C11	−1.91 (12)	C17—N1—C18—O2	−175.69 (8)
C8—C9—C10—C11	179.47 (8)	C19—N1—C18—O2	1.65 (13)
C9—C10—C11—C12	0.91 (13)	C17—N1—C18—C15	4.16 (9)
C10—C11—C12—C13	0.41 (13)	C19—N1—C18—C15	−178.50 (7)
C11—C12—C13—C14	−0.71 (13)	C16—C15—C18—O2	177.49 (8)
C12—C13—C14—C9	−0.29 (12)	C1—C15—C18—O2	57.24 (11)
C12—C13—C14—C1	178.42 (8)	C16—C15—C18—N1	−2.35 (8)
C10—C9—C14—C13	1.61 (12)	C1—C15—C18—N1	−122.60 (7)
C8—C9—C14—C13	−179.62 (7)	C17—N1—C19—C20	87.01 (10)
C10—C9—C14—C1	−177.27 (7)	C18—N1—C19—C20	−90.04 (10)
C8—C9—C14—C1	1.51 (10)	C14—C1—C21—O3	−175.24 (7)
C21—C1—C14—C13	1.20 (11)	C2—C1—C21—O3	63.06 (9)
C2—C1—C14—C13	126.79 (8)	C15—C1—C21—O3	−55.77 (9)
C15—C1—C14—C13	−121.59 (8)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O1ⁱ	0.83 (1)	2.08 (1)	2.8846 (10)	164 (1)

Symmetry code: (i) x, y−1, z.

R.m.s. deviations (Å) of superimposed structures top

	Functional
Basis set	B3LYP	B3LYPD3	APFD	ωB97XD
6-31+G(d,p)	0.1388	0.1441	0.1757	0.1542
6-311+G(2d,p)	0.1342	0.1400	0.1342	0.1550
6-311++G(3df,pd)	0.1345	0.1415	0.1771	0.1559
aug-cc-pVDZ	0.1314	0.1444	0.1802	0.1596

Calculated single point energies and thermochemical corrections of the six possible rotamers in the gas phase in Hartrees top

Rotamer	B2PLYP	B3LYP	ε_ZPE	E_tot	H_corr	G_corr	B3LYP+G_corr	B2PLYP+G_corr
1a	-1091.538475	-1092.214620	0.358477	0.378376	0.379320	0.310435	-1091.904185	-1091.228040
1b	-1091.535152	-1092.210531	0.358047	0.378055	0.378999	0.310221	-1091.900310	-1091.224931
1c	-1091.538449	-1092.215265	0.358913	0.378460	0.379404	0.311802	-1091.903463	-1091.226647
1d	-1091.537743	-1092.214629	0.358441	0.378356	0.379301	0.310398	-1091.904231	-1091.227345
1e	-1091.534218	-1092.210517	0.357923	0.377960	0.378904	0.310029	-1091.900488	-1091.224189
1f	-1091.537691	-1092.215305	0.358738	0.378328	0.379273	0.311384	-1091.903921	-1091.226307

Boltzmann population analysis results of the six rotamers at standard conditions and using the B2PLYPD3/6-311++G(2d,2p)//B3LYP/6-31+G(d,p) level of theory top

Rotamer	Gibbs free energy (Hartree)	Relative Gibbs free energy (kcal mol^-1)	q_i	Fraction (q_i/q)
1a	-1091.228040	0.000000	1.000000	0.518519
1b	-1091.224931	1.950926	0.037910	0.019657
1c	-1091.226647	0.874120	0.230785	0.119666
1d	-1091.227345	0.426119	0.481160	0.249491
1e	-1091.224189	2.416537	0.017361	0.009002
1f	-1091.226307	1.087473	0.161354	0.083665
			q = 1.92857	q = 1

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Search IUCr Journals		doi		Advanced search
Author		volume	page