Introduction
Large amounts of bioactive phenolic compounds are present in the wood knots of several tree species. The amount of lignans in the knots can be up to several hundred times larger than in the adjacent stemwood [
1,
2,
3,
4,
5]. The amount of extractable phenolic compounds is on average around 15% (w/w) in
Picea abies, while
Populus tremula and
Abies balsamea can contain considerable amounts of interesting polyphenols. Those phenolic compounds can be potentially used as antioxidants in food, pharmaceuticals, and natural biocides such as bactericides, pesticides and fungicides [
6]. Additionally, lignans are of great interest in the search for antitumor agents and have potential as chemotherapeutics [
7,
8,
9,
10].
The phenolic compounds are extracted from wood knots and purified by chromatographic methods [
11,
12]. The extract obtained from heartwood, foliage, phloem, bark, and cork of several species is a good resource of natural phenolic antioxidants [
13,
14,
15,
16] but it contains a mixture of different phenolic and nonphenolic compounds in the form of both glycosides and free aglycones. Glycosylation is not desirable, since it affects the antioxidant properties of phenolic compounds [
17]. In comparison, the hydrophilic compounds in knots contain mainly free aglycones of flavonoids and lignans [
1,
2,
3,
4,
5,
18].
Wood knots of
P. tremula and
A. balsamea growing in Europe are rich in dihydrokaempferol (
1) and lariciresinol (
2) (
Figure 1). Dihydrokaempferol - belonging to the flavanones group - shows a capacity to scavenge peroxyl radicals
in vitro. The trapping capacity of that compound (expressed as the number of peroxy radicals in millimoles that are scavenged per gram of extract) is 0.78 mmol/g [
19]. Lignans - among them lariciresinol - also inhibit lipid peroxidation. The trapping capacity of that compound in one of the test series was shown to be 7.3 mmol/g. In comparison, the trapping capacity of a well known antioxidant Trolox
® was reported as 6.8 mmol/g in the same test series [
12]. Lariciresinol also reveals a capacity to scavenge superoxide radicals. Scavenging of superoxide radicals
in vitro expressed as IC
50 values (i.e., concentration of extract required for scavenging of 50% of the radicals) for this compound is 13 μg/L. A X-ray crystallography structural investigation of dihydrokaempferol and lariciresinol is presented in this paper.
Figure 1.
Structural formula of compounds 1 and 2.
Figure 1.
Structural formula of compounds 1 and 2.
Results and Discussion
The crystal structures of two compounds isolated from the European tree species
P. tremula and
A. balsamea are presented here: dihydrokaempferol (3,5,8,13-tetrahydroxyflavanone) (
1) and lariciresinol (3,14-dimethoxy-7,10-epoxylignan-4,15,19-triol) (
2). Their chemical structures are depicted in
Figure 1. The isolation and purification procedures of compound
1 and
2 and their spectroscopic characterization were described earlier [
12,
20]. Crystal data and experimental details for compound
1 and
2 are shown in
Table 1. ORTEP views of the investigated molecules with the atom numbering schemes prepared using the program XP are shown in
Figure 2 [
21].
Two diffraction data sets were collected for
1 with different crystallization solvents and the structure was solved twice:
1a with molecules of ethanol and
1b with molecules of methanol trapped in the crystal lattices. Those are typical "host - guest" type inclusion crystals. The cell parameters
a,
b and
c are similar for both
1a and
1b, which is typical for isostructural solvatomorphs [
22]. The difference in cell volume is 34.5 A
3, which well correlates with the volume of the two methylene groups that distinguish these two structures. The R
obs factor for
1a is significantly higher than that of
1b (
Table 1), so only
1b was further analyzed.
Figure 2.
Thermal ellipsoidal view with the atom numbering scheme of the molecules of 1b and 2.
Figure 2.
Thermal ellipsoidal view with the atom numbering scheme of the molecules of 1b and 2.
The analysis of bond lengths of compound
1 and
2 shows that their values do not differ significantly from typical values for compounds deposited in Cambridge Crystallographic Data Centre [
23]. Elongation of bonds C7-C8, C8-C9, O1-C9 and C9-C10 observed in
1 is typical and caused by asymmetry of heterocyclic ring O1,C1,C6,C7,C8,C9. That ring adopts a conformation halfway between a half-chair and a sofa. In comparison, the five-membered ring of
2 is in a half-chair conformation. The asymmetry parameters indicating the lowest discrepancy from the dominant symmetry elements are shown in
Table 2. The C-C and C-O bonds in the five-membered ring of
2 and also the bonds between carbon atoms (C7, C11) and
m-methoxy-
p-hydroxyphenyl groups of
2 are elongated. The aromatic ring of the hydroxyphenyl substituent can rotate around the C9-C10 bond in the molecule of
1. Free rotation of the aromatic ring of the
m-methoxy-
p-hydroxyphenyl substituent in
2 can occur around only one bond (C1-C7), whilst the second substituent of that type can rotate around two bonds C9-C11 and C11-C12. The values of selected torsion angles of
1 and
2 are presented in
Table 3.
Table 1.
Crystal data and experimental details for compound 1 and 2.
Table 1.
Crystal data and experimental details for compound 1 and 2.
| Compound | 1a | 1b | 2 |
|---|
| Molecular formula | C15H12O6*CH3CH2OH | C15H12O6*CH3OH | C20H24O6 |
| Formula weight | 334.31 | 320.29 | 360.39 |
| CCDC No. | 719360 | 719361 | 719362 |
| Crystallographic system | triclinic | triclinic | monoclinic |
| Space group | P1 | P1 | P21 |
| a [Å] | 7.617(5) | 7.581(2) | 10.718(6) |
| b [Å] | 10.349(3) | 10.275(2) | 5.656(3) |
| c [Å] | 11.488(3) | 11.120(2) | 14.264(8) |
| α [o] | 63.92(2) | 65.28(3) | |
| β [o] | 85.36(4) | 81.80(3) | 92.75(5) |
| γ [o] | 79.18(3) | 76.61(3) | |
| V [Å3] | 798.9(6) | 764.4(3) | 863.7(8) |
| Z | 2 | 2 | 2 |
| Dc [g/cm3] | 1.390 | 1.392 | 1.386 |
| μ [mm-1] | 0.918 | 0.936 | 0.102 |
| Crystal dimensions [mm] | 0.60x0.40x0.02 | 0.56x0.12x0.1 | 1.00x0.06x0.02 |
| Radiation, λ (Å) | CuKα, 1.54178 | CuKα, 1.54178 | synchrotron, 0.80420 |
| hkl ranges: | h = | -9 | 0 | 0 | 9 | -14 | 14 |
| k = | -12 | 12 | -12 | 12 | -6 | 6 |
| l = | -14 | 14 | -13 | 13 | -19 | 19 |
| EAC correction: | min. | 0.8867 | 0.9392 | NA |
| max. | 0.9933 | 0.9980 |
| ave. | 0.9294 | 0.9679 |
| No. of reflections: | unique | 3545 | 3396 | 4342 |
| with
I>0σ(I) | 3353 | 3210 | 3372 |
| obs. with
I>2σ(I) | 2982 | 2982 | 4007 |
| No. of parameters refined | 472 | 454 | 332 |
| Robs | 0.0691 | 0.0430 | 0.0431 |
| wRobs | 0.1871 | 0.1376 | 0.1137 |
| Rint | 0.0000 | 0.0000 | 0.0000 |
| Sobs | 1.098 | 1.094 | 1.051 |
Table 2.
Asymmetry parameters [
24] for heteroatom rings for compound
1b and
2.
Table 2.
Asymmetry parameters [24] for heteroatom rings for compound 1b and 2.
| 1b |
| molecule | 1 | 1’ | molecule | 1 | 1’ |
| ΔCsC6=ΔCsC9 | 12.2(8) | 12.4(8) | ΔC2C1-C6=ΔC2C8-C9 | 13.3(9) | 16.6(9) |
| 2 |
| ΔCsC8 | 11.2(3) | | ΔC2C8-C9 | 4.6(3) | |
| ΔCsC9 | 17.8(3) | | ΔC2C9-C10 | 40.2(3) | |
Table 3.
Selected torsion angles (°) for compounds 1b and 2.
Table 3.
Selected torsion angles (°) for compounds 1b and 2.
| 1b |
| molecule | 1 | 1’ | molecule | 1 | 1’ |
| C1 | C2 | C3 | O2 | -177.3(3) | -179.2(4) | C1 | O1 | C9 | C10 | 172.7(3) | -179.7(3) |
| O2 | C3 | C4 | C5 | 176.5(3) | -179.7(4) | O5 | C8 | C9 | C10 | 60.4(4) | 54.0(4) |
| C3 | C4 | C5 | O3 | -178.7(3) | 179.1(3) | C7 | C8 | C9 | C10 | -176.4(3) | 176.8(3) |
| O3 | C5 | C6 | C1 | 180.0(3) | -178.8(3) | O1 | C9 | C10 | C15 | -65.8(4) | -66.5(4) |
| O3 | C5 | C6 | C7 | 2.9(5) | 4.4(5) | C8 | C9 | C10 | C15 | 52.8(5) | 53.1(5) |
| C6 | C7 | C8 | O5 | 160.4(3) | 161.4(3) | O1 | C9 | C10 | C11 | 118.9(4) | 114.5(4) |
| C5 | C6 | C7 | O4 | -7.3(6) | -7.6(6) | C8 | C9 | C10 | C11 | -122.4(4) | -125.9(4) |
| O4 | C7 | C8 | O5 | -22.5(5) | -20.0(5) | O6 | C13 | C14 | C15 | 179.4(5) | -179.5(4) |
| O4 | C7 | C8 | C9 | -144.9(3) | -142.1(3) | | | | | | |
| 2 |
| C18 | O2 | C3 | C2 | 0.4(2) | | O1 | C7 | C8 | C19 | -88.0(1) | |
| C18 | O2 | C3 | C4 | 179.8(1) | | C1 | C7 | C8 | C19 | 149.7(1) | |
| O2 | C3 | C4 | O3 | -0.1(2) | | O1 | C7 | C8 | C9 | 33.6(1) | |
| C2 | C3 | C4 | O3 | 179.3(1) | | C19 | C8 | C9 | C11 | -43.2(2) | |
| O2 | C3 | C4 | C5 | 180.0(1) | | C9 | C11 | C12 | C17 | 84.7(2) | |
| O3 | C4 | C5 | C6 | -178.6(1) | | C9 | C11 | C12 | C13 | -92.5(2) | |
| C10 | O1 | C7 | C1 | 107.9(1) | | C20 | O4 | C14 | C13 | -0.2(2) | |
| C10 | O1 | C7 | C8 | -15.4(1) | | C20 | O4 | C14 | C15 | 177.7(1) | |
| C6 | C1 | C7 | O1 | -19.2(2) | | C12 | C13 | C14 | O4 | -179.6(1) | |
| C2 | C1 | C7 | O1 | 162.0(1) | | O4 | C14 | C15 | O5 | -1.1(2) | |
| C6 | C1 | C7 | C8 | 99.3(2) | | C7 | C8 | C19 | O6 | -67.7(2) | |
| C2 | C1 | C7 | C8 | -79.4(2) | | | | | | | |
The values of dihedral angles between the planes of the rings of
1 and
2 are presented in
Table 4. Plane 2 passing through the atoms of the hydroxyphenyl substituent is almost perpendicular to the plane of the heterocyclic ring in
1.
Table 4.
Dihedral angles between the planes passing through selected atoms for compounds 1b and 2.
Table 4.
Dihedral angles between the planes passing through selected atoms for compounds 1b and 2.
| 1b | 2 |
|---|
| Plane 1 C1, C2, C3, C4, C5, C6 | Plane 1 C1, C2, C3, C4, C5, C6 |
| Plane 2 C10, C11, C12, C13, C14, C15 | Plane 2 C12, C13, C14, C15, C16, C17 |
| Plane 3 C7, C8, C9 | Plane 3 O1, C7, C9, C10 |
| Plane 4 O1, C8, C9 | Plane 4 C7, C8, C9 |
| Plane 5 O1, C1, C6, C7 | Plane 5 O1, C7, C10 |
| molecule | 1 | 1’ | | |
| 1 / 2 | 85.76(14) | 87.22(16) | 1 / 2 | 38.61(4) |
| 1 / 3 | 38.63(38) | 40.55(22) | 1 / 3 | 86.53(5) |
| 2 / 3 | 56.54(36) | 52.61(25) | 2 / 3 | 55.71(5) |
| 1 / 4 | 44.27(39) | 50.10(21) | 1 / 4 | 68.13(7) |
| 2 / 4 | 88.23(19) | 89.68(23) | 2 / 4 | 75.63(8) |
| 3 / 4 | 58.58(42) | 63.41(28) | 3 / 4 | 36.70(10) |
| 1 / 5 | 3.06(20) | 3.02(18) | 1 / 5 | 80.48(8) |
| 2 / 5 | 88.57(20) | 89.78(17) | 2 / 5 | 61.55(8) |
| 3 / 5 | 35.64(42) | 37.53(28) | 3 / 5 | 6.16(9) |
| 4 / 5 | 45.21(38) | 50.32(20) | 4 / 5 | 32.72(12) |
Similarly, Plane 1 (passing through the atoms of one of the m-methoxy-p-hydroxyphenyl group) is almost perpendicular to Plane 3 (passing through atoms O1, C7, C9, C10) in 2. In comparison Plane 2 (passing through the atoms of the second m-methoxy-p-hydroxyphenyl group) is inclined to Plane 3 at an angle of 55.71(5)° in 2.
Figure 3 shows the crystal packing and
Figure 4 presents the intermolecular interactions in the crystal lattices of
1a,
1b, and
2. The conformations of the molecules depend on the net of hydrogen bonds and π-stacking hydrophobic interactions influenced by the presence of solvent molecules. The hydrogen-bonding geometry for compounds
1 and
2 is shown in
Table 5. Molecules of
1 create strong hydrogen bonds with the solvent molecules (
1a with methanol and
1b with ethanol, respectively). There are also two intramolecular hydrogen bonds O3−H3O···O4, O5−H5O···O4 and a few intermolecular hydrogen bonds in the crystal lattice of
1. π-stacking interactions between aromatic rings of the molecules from neighboring unit cells are important factors determining the crystal packing of compound
2. There are also two intramolecular hydrogen bonds O3−H3O···O2, O5−H5O···O4, and three intermolecular hydrogen bonds: O6−H6O···O1, O5−H5O···O6 in the crystal lattice of compound
2.
Figure 3.
Crystal packing diagram for 1 and 2.
Figure 3.
Crystal packing diagram for 1 and 2.
Figure 4.
Intermolecular interactions in the crystal lattices of 1 and 2 (hydrogens attached to carbon atoms are omitted for clarity).
Figure 4.
Intermolecular interactions in the crystal lattices of 1 and 2 (hydrogens attached to carbon atoms are omitted for clarity).
Table 5.
Hydrogen-bonding geometry (Å, °) (H···A not greater then 2.55Å) for 1 and 2.
Table 5.
Hydrogen-bonding geometry (Å, °) (H···A not greater then 2.55Å) for 1 and 2.
| D―H···A | D―H | H···A | D···A | D―H···A |
| 1a |
| O3―H3O···O4 | 0.820(27) | 1.926(30) | 2.646(5) | 146.0(36) |
| O5―H5O···O4 | 0.820(26) | 2.265(28) | 2.698(5) | 113.4(28) |
| O3'―H3'O···O4' | 0.820(14) | 1.955(34) | 2.656(5) | 143.0(35) |
| O5'―H5'O···O4' | 0.820(23) | 2.231(20) | 2.701(4) | 116.7(23) |
| O5―H5O···O4' i | 0.820(26) | 2.068(33) | 2.767(5) | 142.9(31) |
| O6―H6O···O5' ii | 0.820(36) | 1.895(39) | 2.698(6) | 165.7(45) |
| O5'―H5'O···O4 iii | 0.820(23) | 2.088(20) | 2.751(4) | 137.7(25) |
| O6'―H6'O···O5 iv | 0.820(43) | 1.929(44) | 2.663(7) | 148.7(40) |
| O2―H2O···O7 v | 0.820(42) | 1.814(46) | 2.616(6) | 165.6(59) |
| O7―H7O···O6vi | 0.820(18) | 2.005(32) | 2.796(7) | 161.8(63) |
| O2'―H2'O···O7' vii | 0.820(19) | 1.934(56) | 2.630(6) | 142.1(42) |
| O7'―H7'O···O6' viii | 0.820(16) | 2.008(22) | 2.817(7) | 168.7(38) |
| C8―H8···O2 vii | 0.980(8) | 2.406(6) | 3.133(7) | 130.5(5) |
| 1b |
| O3―H3O···O4 | 0.820(18) | 1.925(22) | 2.646(4) | 146.3(28) |
| O5―H5O···O4 | 0.820(23) | 2.303(27) | 2.689(4) | 109.4(28) |
| O3'―H3'O···O4' | 0.820(14) | 1.945(23) | 2.665(4) | 146.0(28) |
| O5'―H5'O···O4' | 0.820(21) | 2.257(23) | 2.698(3) | 114.1(23) |
| O5―H5O···O4' i | 0.820(23) | 2.104(35) | 2.773(4) | 138.5(32) |
| O6―H6O···O5' ii | 0.820(25) | 1.871(26) | 2.676(4) | 166.5(30) |
| O5'―H5'O···O4 iii | 0.820(21) | 2.066(13) | 2.762(3) | 142.5(26) |
| O6'―H6'O···O5 iv | 0.820(52) | 1.893(52) | 2.651(5) | 153.2(51) |
| O2―H2O···O7 v | 0.820(18) | 1.815(19) | 2.627(4) | 169.9(20) |
| O7―H7O···O6 vi | 0.820(38) | 1.979(33) | 2.769(5) | 161.4(43) |
| O2'―H2'O···O7' vii | 0.820(49) | 1.809(49) | 2.626(5) | 174.3(57) |
| O7'―H7'O···O6' viii | 0.820(18) | 1.995(19) | 2.789(6) | 162.6(33) |
| C8―H8···O2 vii | 0.980(6) | 2.441(5) | 3.124(5) | 126.5(4) |
| 2 |
| O3―H3O···O2 | 0.889(30) | 2.128(30) | 2.652(2) | 117.0(24) |
| O5―H5O···O4 | 0.874(35) | 2.187(27) | 2.660(2) | 113.6(26) |
| O6―H6O···O1ix | 0.975(31) | 1.848(30) | 2.787(2) | 160.8(27) |
| O5―H5O···O6 i | 0.874(35) | 2.312(28) | 2.880(2) | 122.7(27) |
| C2―H2···O5 iii | 1.075(24) | 2.386(24) | 3.454(2) | 172.3(18) |
| C13―H13···O6 x | 1.018(23) | 2.546(24) | 3.452(2) | 148.1(19) |
| C20―H201···O4 xi | 0.965(30) | 2.544(28) | 3.464(3) | 159.5(22) |
