Structure determination of riboflavin by synchrotron high-resolution powder X-ray diffraction

Guerain, M.; Affouard, F.; Henaff, C.; Dejoie, C.; Danède, F.; Siepmann, J.; Siepmann, F.; Willart, J.-F.

doi:10.1107/S2053229621012171

Structure determination of riboflavin by synchrotron high-resolution powder X-ray diffraction

M. Guerain, F. Affouard, C. Henaff, C. Dejoie, F. Danède, J. Siepmann, F. Siepmann and J.-F. Willart

The crystal structure of the stable form of vitamin B2 or riboflavin (C₁₇H₂₀N₄O₆) was solved using high-resolution powder X-ray diffraction (PXRD). The high-resolution PXRD pattern of riboflavin was recorded at room temperature at the European Synchrotron Radiation Facility (Grenoble, France). The starting structural model was generated using a Monte Carlo simulated annealing method. The final structure was obtained through Rietveld refinement. The positions of the H atoms belonging to hydroxy groups were estimated from computational energy minimizations. The symmetry is orthorhombic with the space group P2₁2₁2₁ and the following lattice parameters: a = 20.01308, b = 15.07337 and c = 5.31565 Å.

Keywords: powder diffraction; crystal structure; riboflavin; Monte Carlo simulated annealing; computational energy minimization; API; synchrotron.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229621012171/vp3020sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S2053229621012171/vp3020Isup2.hkl Contains datablock I
	Rietveld powder data file (CIF format) https://doi.org/10.1107/S2053229621012171/vp3020Isup3.rtv Contains datablock I
	Text file https://doi.org/10.1107/S2053229621012171/vp3020sup4.txt CIF with all atoms optimized by DFT. Structure is close to that submitted, so it confirms the structure submitted where dFT were performed on O and H atoms especially. This cif have R factors too high after Rietveld, so it confirms the cif submitted but it is not chosen as the best CIF

CCDC reference: 2122541

Computing details top

\ 7,8-Dimethyl-10-[(2R,3R,4S)-2,3,4,5-tetrahydroxypentyl]\ benzo[g]pteridine-2,4(3H,10H)-dione top

Crystal data top

C₆₈H₈₀N₁₆O₂₄	V = 1603.54 (2) Å³
M_r = 1505.5	Z = 1
Orthorhombic, P2₁2₁2₁	F(000) = 792
Hall symbol: P 2xab;2ybc;2zac	D_x = 1.559 Mg m⁻³
a = 20.01308 (15) Å	Synchrotron radiation
b = 15.07337 (12) Å	T = 293 K
c = 5.31565 (4) Å	orange

Data collection top

Synchrotron
diffractometer

2θ_min = 1.5°, 2θ_max = 12°, 2θ_step = 0.001°

Refinement top

R_p = 0.084	0 restraints
R_wp = 0.113	0 constraints
R_exp = 0.036	H-atom parameters constrained
R(F) = 0.125	Weighting scheme based on measured s.u.'s
10501 data points	(Δ/σ)_max = 0.042
Profile function: Pseudo-Voigt	Background function: 8 Legendre polynoms
18 parameters	Preferred orientation correction: none

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.08278	0.02019	0.34375	0.0422*
O2	0.14877	0.17673	0.1441	0.0422*
O3	0.1782	0.00367	−0.30786	0.0422*
O4	0.2585	0.15191	−0.4911	0.0422*
O5	−0.18857	−0.1883	−0.14607	0.0422*
O6	−0.00119	−0.14281	−0.63307	0.0422*
N7	−0.0342	0.05621	0.01071	0.0422*
N8	−0.15114	−0.04125	0.12809	0.0422*
N9	−0.01887	−0.04842	−0.32105	0.0422*
N10	−0.09618	−0.16737	−0.39024	0.0422*
C11	0.07628	0.04441	0.08517	0.0422*
C12	0.02745	0.09824	−0.07628	0.0422*
C13	0.1459	0.08712	0.0583	0.0422*
C14	0.17662	0.09153	−0.20707	0.0422*
C15	−0.07468	0.08311	0.21446	0.0422*
C16	−0.05221	−0.01772	−0.13003	0.0422*
C17	−0.13261	0.03352	0.26915	0.0422*
C18	−0.06043	0.15703	0.36703	0.0422*
C19	−0.115	−0.06582	−0.05558	0.0422*
C20	0.24751	0.12748	−0.23832	0.0422*
C21	−0.10212	0.18092	0.56672	0.0422*
C22	−0.17413	0.05808	0.47014	0.0422*
C23	−0.15899	0.13144	0.61835	0.0422*
C24	−0.13836	−0.14599	−0.19538	0.0422*
C25	−0.08446	0.26007	0.72221	0.0422*
C26	−0.19914	0.16405	0.83614	0.0422*
C27	−0.03807	−0.12201	−0.4569	0.0422*
H28	0.0753	−0.02438	0.01942	0.0844*
H30	0.0256	0.16899	−0.02712	0.0844*
H29	0.03236	0.09849	−0.28129	0.0844*
H31	0.18212	0.05117	0.17488	0.0844*
H32	0.14479	0.13134	−0.33112	0.0844*
H33	−0.01711	0.19856	0.3321	0.0844*
H34	0.25377	0.19418	−0.16174	0.0844*
H35	0.28442	0.08334	−0.15236	0.0844*
H36	−0.21862	0.01891	0.5092	0.0844*
H37	0.05569	−0.03376	0.37017	0.0844*
H38	0.1827	0.17751	0.28129	0.0844*
H39	0.14921	0.00731	−0.46058	0.0844*
H40	−0.03823	0.29162	0.65755	0.0844*
H41	−0.12394	0.31018	0.7116	0.0844*
H42	−0.0767	0.241	0.91873	0.0844*
H43	−0.24335	0.12276	0.86886	0.0844*
H44	−0.16945	0.16268	1.00905	0.0844*
H45	−0.21685	0.23171	0.80197	0.0844*
H46	−0.10838	−0.22121	−0.49571	0.0844*
H47	0.24692	0.21388	−0.49935	0.0844*

Geometric parameters (Å, º) top

O1—C11	1.4281 (1)	C13—C14	1.5402 (1)
O1—H37	0.9874 (1)	C13—H31	1.0969
O2—C13	1.4268 (1)	C14—C20	1.5278 (1)
O2—H38	0.9965	C14—H32	1.0958
O3—C14	1.4290 (1)	C15—C17	1.4097 (1)
O3—H39	0.9993 (1)	C15—C18	1.4073 (1)
O4—C20	1.4105 (1)	C16—C19	1.5038 (1)
O4—H47	0.9600 (1)	C17—C22	1.4032 (1)
O5—C24	1.2187 (1)	C18—C21	1.3973 (1)
O6—C27	1.2329 (1)	C18—H33	1.0854 (1)
N7—C12	1.4620 (1)	C19—C24	1.4937 (1)
N7—C15	1.4120 (1)	C20—H34	1.0919 (1)
N7—C16	1.3898 (1)	C20—H35	1.0941
N8—C17	1.4036 (1)	C21—C23	1.3882 (1)
N8—C19	1.2702 (1)	C21—C25	1.4938 (1)
N9—C16	1.3001 (1)	C22—C23	1.3911 (1)
N9—C27	1.3782 (1)	C22—H36	1.0883 (1)
N10—C24	1.3745 (1)	C23—C26	1.4925 (1)
N10—C27	1.3948 (1)	C25—H40	1.0956 (1)
N10—H46	1.0161 (1)	C25—H41	1.0945 (1)
C11—C12	1.5329 (1)	C25—H42	1.0945 (1)
C11—C13	1.5415 (1)	C26—H43	1.0957 (1)
C11—H28	1.0944 (1)	C26—H44	1.0947 (1)
C12—H30	1.0986 (1)	C26—H45	1.0949 (1)
C12—H29	1.0942 (1)

C11—O1—H37	107.3025 (1)	N8—C17—C15	122.2009 (3)
C13—O2—H38	105.8145 (2)	N8—C17—C22	117.5258 (3)
C14—O3—H39	103.9365 (2)	C15—C17—C22	120.2733 (3)
C20—O4—H47	102.1133 (2)	C15—C18—C21	121.3861 (3)
C12—N7—C15	127.0389 (3)	C15—C18—H33	121.3277 (3)
C12—N7—C16	113.3331 (3)	C21—C18—H33	117.2758 (3)
C15—N7—C16	119.6280 (3)	N8—C19—C16	122.5147 (3)
C17—N8—C19	119.6233 (3)	N8—C19—C24	116.1079 (3)
C16—N9—C27	123.5440 (3)	C16—C19—C24	121.3774 (3)
C24—N10—C27	126.0548 (3)	O4—C20—C14	109.94
C24—N10—H46	117.0943 (3)	O4—C20—H34	95.5592 (3)
C27—N10—H46	116.8510 (3)	O4—C20—H35	116.8289 (2)
O1—C11—C12	137.0727 (1)	C14—C20—H34	113.1172 (2)
O1—C11—C13	96.5236 (1)	C14—C20—H35	111.4603 (5)
O1—C11—H28	93.8303 (3)	H34—C20—H35	109.0728 (4)
C12—C11—C13	107.6548 (4)	C18—C21—C23	120.0851 (3)
C12—C11—H28	108.1367 (4)	C18—C21—C25	119.0038 (3)
C13—C11—H28	112.4765 (2)	C23—C21—C25	120.9111 (3)
N7—C12—C11	97.5593 (5)	C17—C22—C23	120.7923 (3)
N7—C12—H30	108.4797 (3)	C17—C22—H36	119.1170 (3)
N7—C12—H29	113.0967 (1)	C23—C22—H36	120.0907 (3)
C11—C12—H30	113.7113 (3)	C21—C23—C22	119.5835 (3)
C11—C12—H29	120.1427 (3)	C21—C23—C26	114.6973 (3)
H30—C12—H29	103.6849 (1)	C22—C23—C26	125.7193 (3)
O2—C13—C11	113.7119 (2)	O5—C24—N10	123.0772 (3)
O2—C13—C14	103.6406 (2)	O5—C24—C19	125.0607 (3)
O2—C13—H31	105.0993 (4)	N10—C24—C19	111.8621 (3)
C11—C13—C14	117.6252 (2)	C21—C25—H40	111.8947 (3)
C11—C13—H31	109.7952 (4)	C21—C25—H41	110.6007 (4)
C14—C13—H31	105.9598 (4)	C21—C25—H42	110.6036 (4)
O3—C14—C13	108.1930 (2)	H40—C25—H41	107.0916 (5)
O3—C14—C20	105.5103 (2)	H40—C25—H42	107.0733 (2)
O3—C14—H32	107.1440 (4)	H41—C25—H42	109.4413 (1)
C13—C14—C20	119.0501 (1)	C23—C26—H43	111.7659 (3)
C13—C14—H32	110.0430 (4)	C23—C26—H44	110.6617 (5)
C20—C14—H32	106.2713 (4)	C23—C26—H45	110.6332 (3)
N7—C15—C17	118.5391 (3)	H43—C26—H44	107.1175 (3)
N7—C15—C18	123.5812 (3)	H43—C26—H45	107.1007 (5)
C17—C15—C18	117.8797 (3)	H44—C26—H45	109.4257 (1)
N7—C16—N9	124.9396 (3)	O6—C27—N9	115.8322 (3)
N7—C16—C19	117.4939 (3)	O6—C27—N10	124.5726 (3)
N9—C16—C19	117.5665 (3)	N9—C27—N10	119.5952 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C20—H34···O5ⁱ	1.09	2.43	3.0789	116.98
C20—H35···O3ⁱⁱ	1.09	2.37	3.3696	150.58
O1—H37···O6ⁱⁱⁱ	0.99	2.00	2.9792	171.27
O1—H37···N9ⁱⁱⁱ	0.99	2.23	2.8953	123.63
O1—H37···C27ⁱⁱⁱ	0.99	2.48	3.4010	155.65
O2—H38···O4ⁱⁱⁱ	1.00	1.98	2.9534	165.41
O3—H39···O1^iv	1.00	1.70	2.6718	163.30
O4—H47···O5ⁱ	1.00	1.95	2.8795	153.19
C26—H44···C15ⁱⁱⁱ	1.09	2.50	3.4259	142.09
C26—H44···C17ⁱⁱⁱ	1.09	2.50	3.3079	129.74
C26—H45···O4^v	1.09	2.46	3.4320	147.21
N10—H46···O2^vi	1.02	1.91	2.9070	166.80

Symmetry codes: (i) −x, y+1/2, −z−1/2; (ii) −x+1/2, −y, z+1/2; (iii) x, y, z+1; (iv) x, y, z−1; (v) x−1/2, −y+1/2, −z; (vi) −x, y−1/2, −z−1/2.

Crystallographic data, profile and structural parameters for riboflavin obtained after Rietveld refinement top

Crystal data
Chemical formula	C₁₇H₂₀N₄O₆
M_r	376.37
Cell setting, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	293
a,b,c (Å)	20.01308 (15), 15.07337 (12), 5.31565 (4)
V (Å³)	1603.54 (2)
Z	4
F(000)	792
µ (mm^-1)	0.04
Specimen shape, size (mm)	Cylinder, 1
2θ range (°)	0–12

Data collection
Beamline	ID22 (ESRF)
Specimen mounting	1 mm diameter glass capillary
Data collection mode	Transmission
Scan method	Continuous scan
Radiation type	Synchrotron 35 KeV, λ = 0.354196 Å
Binning size (°2θ)	0.001

Refinement
R factors and goodness of fit	R = 0.0837, R_wp = 0.1125, R_exp = 0.0355

Comparison of the bonds, angles and torsion angles between riboflavin obtained in this work, adenine–riboflavin trihydrate (ADRBFT10) and the complex riboflavin–5'-bromo-5'-deoxyadenosine trihydrate (RIBBAD) top

Riboflavin	This work	Computed	RIBBAD	ADRBFT10
Bonds
C23—C26	1.492	1.4929	1.568	1.597
C21—C25	1.493	1.4940	1.671	1.622
N7—C12	1.462	1.4621	1.439	1.546
C12—C11	1.532	1.5332	1.523	1.554
C11—C13	1.541	1.5416	1.476	1.614
C13—C14	1.540	1.5405	1.636	1.569
C14—C20	1.527	1.5281	1.487	1.612
C20—O4	1.410	1.4241	1.439	1.667
C13—O2	1.426	1.4270	1.316	1.478
C14—O3	1.428	1.4290	1.355	1.621
C11—O1	1.428	1.4283	1.419	1.551
C24—O5	1.218	1.2189	1.168	1.203
C27—O6	1.232	1.2331	1.214	1.231

Angles
C15—N7—C12	127.03	118.14	127.11	121.40
C16—N7—C12	113.33	121.71	119.40	118.02
N7—C12—C11	97.55	110.02	116.53	105.85
C12—C11—C13	107.65	112.64	114.89	108.25
C11—C13—C14	117.62	113.03	109.62	114.36
C13—C14—C20	119.05	112.36	112.22	114.15
C14—C20—O4	109.94	108.78	120.05	105.71
C13—C14—O3	108.19	109.07	105.53	100.50
O2—C13—C14	113.71	108.65	110.84	100.50
C12—C11—O1	137.07	108.56	107.15	108.71
C22—C23—C26	125.71	119.24	114.12	120.97
C21—C23—C26	114.69	121.18	113.89	121.95
C23—C21—C25	120.91	120.91	130.30	119.46
C18—C21—C25	119.00	119.01	103.91	117.55
C19—C24—O5	125.06	120.61	125.12	120.79
N10—C24—O5	123.07	127.52	123.51	124.93
N10—C27—O6	124.57	119.22	121.15	109.51
N9—C27—O6	115.83	121.17	121.14	127.18

Torsion angles
C11—C12—N7—C15	90.66	-90	88.38	99.45
O1—C11—C12—N7	-49.93	-58.65	-54.54	-74.90
O2—C13—C11—C12	61.4	-58.35	-53.16	178.73
O3—C14—C13—C11	-55.47	178.94	-49.04	-73.09
O4—C20—C14—C13	-161.74	-178.54	-172.38	40

Comparison of lattice parameters (Å, °) between riboflavin obtained in this work, adenine–riboflavin trihydrate (ADRBFT10) and the complex riboflavin–5'-bromo-5'-deoxyadenosine trihydrate (RIBBAD) top

Structure	a	b	c	β	V (Å³)	Symmetry	Reference
Riboflavin	20.01308	15.07337	5.31565	90	1603.54	Orthorombic P2₁2₁2₁	This work
RIBBAD	7.773	8.628	47.934	90	3214.71	Orthorombic P2₁2₁2₁	Voet & Rich (1971)
ADRBFT10	8.53	7.88	37.82	97.83	2518.42	Monoclinic P2₁	Fujii et al. (1977)

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