Charge-density analysis using multipolar atom and spherical charge models: 2-methyl-1,3-cyclopent­anedione, a compound displaying a resonance-assisted hydrogen bond

The experimental charge-density distribution in 2-methyl-1,3-cyclopentanedione in the crystal state was analyzed by synchrotron X-ray diffraction data collection at 0.33 Å resolution. The molecule in the crystal is in the enol form. The experimental electron density was refined using the Hansen–Coppens multipolar model and an alternative modeling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites. The crystallographic refinements, charge-density distributions, molecular electrostatic potentials, dipole moments and intermolecular interaction energies obtained from the different charge-density models were compared. The experimental results are also compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculations at the B3LYP/6-31G** level. A strong intermolecular O—H...O hydrogen bond connects molecules along the [001] direction. The deformation density maps show the resonance within the O=C—C=C—OH fragment and merged lone pair lobes on the hydroxyl O atom. This resonance is further confirmed by the analysis of charges and topology of the electron density.

Computing details

Program(s) used to refine structure: MoPro (J. Appl. Cryst. 2005, 38, 38-54); molecular graphics: MoproViewer.

Figures

2-methyl-1,3-cyclopentanedione

Crystal data

C6H8O2	Z = 4
Mr = 112.13	F(000) = 240
Monoclinic, C2/m	Dx = 1.472 Mg m^−3
Hall symbol: -c_2y	Synchrotron radiation, λ = 0.21784 Å
a = 12.402 (3) Å	µ = 0.001 mm^−1
b = 6.470 (2) Å	T = 100 K
c = 6.321 (2) Å	, colourless
β = 93.69 (2)°	0.3 × 0.2 × 0.1 mm
V = 506.2 (3) Å^3

Data collection

Huber, ID11/ESRF diffractometer	θmax = 19.3°, θmin = 1.0°
258713 measured reflections	h = −37→36
7435 independent reflections	k = 0→19
7319 reflections with > 2.0σ(I)	l = 0→19
Rint = 0.049

Refinement

Refinement on F	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.034	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.031	Only H-atom coordinates refined
S = 1.05	w = 1/[93.*σ^2(Fo^2)]
7434 reflections	(Δ/σ)max < 0.001
186 parameters	Δρmax = 0.55 e Å^−3
15 restraints	Δρmin = −0.36 e Å^−3

Special details

Refinement. Refinement of F¹ against reflections. The threshold expression of F² > σ(F²) is used for calculating R-factors(gt) 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 (Ų)

	x	y	z	Uiso*/Ueq
O1	0.30499 (2)	0	1.06772 (3)	0.0162 (2)
O3	0.178900 (10)	0	0.36827 (2)	0.0129 (2)
C1	0.302450 (10)	0	0.87585 (2)	0.0109 (2)
C2	0.210221 (1)	0	0.73478 (2)	0.0100 (2)
C3	0.243333 (1)	0	0.53737 (2)	0.0095 (2)
C4	0.361518 (1)	0	0.52858 (2)	0.0110 (2)
C5	0.401380 (10)	0	0.75687 (2)	0.0144 (2)
C21	0.100080 (10)	0	0.80244 (2)	0.0142 (2)
H3	0.22210	0	0.23608	0.02464
H4	0.38786	0.13621	0.44339	0.02701
H5	0.45004	0.13600	0.79766	0.03256
H21A	0.04227	0	0.67142	0.03257
H21B	0.08455	0.13300	0.89305	0.03115

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0156 (6)	0.0253 (6)	0.0078 (6)	0	0.00156 (5)	0
O3	0.0117 (6)	0.0178 (6)	0.0091 (6)	0	−0.000006 (4)	0
C1	0.0109 (6)	0.0143 (6)	0.0077 (6)	0	0.00152 (4)	0
C2	0.0094 (6)	0.0122 (6)	0.0085 (6)	0	0.00215 (4)	0
C3	0.0096 (6)	0.0111 (6)	0.0080 (6)	0	0.00136 (4)	0
C4	0.0101 (6)	0.0140 (6)	0.0091 (6)	0	0.00234 (4)	0
C5	0.0099 (6)	0.0235 (6)	0.0099 (6)	0	0.00083 (4)	0
C21	0.0108 (6)	0.0180 (6)	0.0142 (6)	0	0.00403 (5)	0
H3	0.0230	0.0353	0.0158	0	0.0024	0
H4	0.0263	0.0262	0.0291	−0.0049	0.0058	0.0074
H5	0.0295	0.0412	0.0265	−0.0138	−0.0023	−0.0041
H21A	0.0217	0.0492	0.0262	0	−0.0030	0
H21B	0.0339	0.0293	0.0314	0.0036	0.0117	−0.0056

Geometric parameters (Å, º)

O1—C1	1.2112 (4)	C3—C4	1.4704 (4)
O3—C3	1.2927 (4)	C4—C5	1.4950 (5)
O3—H3	1.021	C4—H4	1.094
C1—C2	1.4043 (4)	C5—H5	1.088
C1—C5	1.4798 (4)	C21—H21B	1.058
C2—C3	1.3385 (4)	C21—H21A	1.060
C2—C21	1.4574 (4)
O1—C1—C2	127.12 (6)	C2—C21—H21B	111.4
O1—C1—C5	122.68 (5)	C2—C21—H21A	111.7
O3—C3—C2	124.09 (3)	C3—O3—H3	110.3
O3—C3—C4	122.23 (4)	C3—C2—C21	128.55 (4)
C1—C2—C3	107.80 (4)	C3—C4—C5	103.42 (4)
C1—C2—C21	123.65 (3)	C3—C4—H4	110.4
C1—C5—C4	104.90 (4)	C4—C5—H5	111.9
C1—C5—H5	110.2	C5—C4—H4	112.6
C2—C3—C4	113.68 (2)	H21A—C21—H21B	106.6
C2—C1—C5	110.21 (4)
O1—C1—C2—C3	180	C2—C3—O3—H3	180
O1—C1—C2—C21	0	C2—C3—C4—C5	0
O1—C1—C5—C4	180	C2—C3—C4—H4	−120.7
O1—C1—C5—H5	−59.4	C2—C1—C5—C4	0
O3—C3—C2—C1	180	C2—C1—C5—H5	120.6
O3—C3—C2—C21	0	C3—C2—C1—C5	0
O3—C3—C4—C5	180	C3—C2—C21—H21B	−119.1
O3—C3—C4—H4	59.3	C3—C2—C21—H21A	0
C1—C2—C3—C4	0	C3—C4—C5—H5	−119.4
C1—C2—C21—H21B	60.9	C4—C3—O3—H3	0
C1—C2—C21—H21A	180	C4—C3—C2—C21	180
C1—C5—C4—C3	0	C5—C1—C2—C21	180
C1—C5—C4—H4	119.2	H4—C4—C5—H5	−0.2

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O3—H3···O1^i	1.021	1.526	2.5370 (6)	169.4

Symmetry code: (i) x, y, z−1.