Crystal structures of 1,1,1-trifluoro-4-hydroxy-4-phenyl-but-3-EN-2-one, 2,2,6,6-tetramethyl-3-hydroxy-hept-3-EN-5-one, 2,2,6,6- tetramethyl-3- methylamino-hept-3-EN-5-one and a study of the ability of these ligands to complex formation with metals

Article abstract of DOI:10.1134/S0022476612040178

Crystal structures are determined (Bruker Nonius X8 Apex, 4K CCD-detector, λMoKα, graphite monochromator, T 150 K and 293 K) for two β-diketones F₃CC(O)CH₂C(O)Ph (1) (space group P2 ₁/c, a = 7.0713(3) A, b = 11.5190(6) A, c = 11.3602(6) A, β = 99.405(2)°, V = 912.90(8) A³, Z = 4), (CH₃) ₃CC(O)CH₂C(O)C(CH₃)₃ (2) (space group Pbca, a = 11.5536(8) A, b = 11.5796(10) A, c = 17.2523(13) A, V = 2308.1(3) A³, Z = 8) and a ketoimine (CH₃) ₃CC(NCH₃)CH₂C(O)C(CH₃)₃ (3) (space group I41/a, a = 18.7687(6) A, b = 18.7687(6) A, c = 14.5182(6) A, V = 5114.2(3) A³, Z = 16). All structures are molecular and comprise isolated molecules joined by van der Walls interactions. The substitution energy of a Na atom for a hydrogen atom in free ligands is calculated by the hybrid B3LYP quantum chemical method. A successful preparation of Na(I) chelates with ligands 1, 2 and failed attempts to prepare a complex with ligand 3 are in accordance with the calculations. Geometrical simulation of a copper(II) complex with ligand 3 reveals the overlap of CH₃ groups which hinders the complexation. Original Russian Text Copyright

Full text of DOI:10.1134/S0022476612040178

Journal of Structural Chemistry. Vol. 53, No. 4, pp. 740-747, 2012
Original Russian Text Copyright © 2012 by P. A. Stabnikov, L. G. Bulusheva,
N. I. Alferova, A. I. Smolentsev, I. A. Korol’kov, N. V. Pervukhina, I. A. Baidina
Devoted to the Jubilee of Academician F. A. Kuznetsov
CRYSTAL STRUCTURES OF 1,1,1-TRIFLUORO-4-
HYDROXY-4-PHENYL-BUT-3-EN-2-ONE, 2,2,6,6-
TETRAMETHYL-3-HYDROXY-HEPT-3-EN-5-ONE,
2,2,6,6- TETRAMETHYL-3-METHYLAMINO-HEPT-
3-EN-5-ONE AND A STUDY OF THE ABILITY OF THESE
LIGANDS TO COMPLEX FORMATION WITH METALS
©
P. A. Stabnikov, L. G. Bulusheva, N. I. Alferova,
A. I. Smolentsev, I. A. Korol’kov, N. V. Pervukhina,
and I. A. Baidina
UDC 548.737:541.49
Crystal structures are determined (Bruker Nonius X8 Apex, 4К CCD-detector, λMoK , graphite
α
monochromator, T 150 K and 293 K) for two β-diketones F3CC(O)CH2C(O)Ph (1) (space group P21/c,
3
a = 7.0713(3) Å, b = 11.5190(6) Å, c = 11.3602(6) Å, β = 99.405(2)°, V = 912.90(8) Å , Z = 4),
(CH3)3CC(O)CH2C(O)C(CH3)3 (2) (space group Pbca, a = 11.5536(8) Å, b = 11.5796(10) Å, c =
3
17.2523(13) Å, V = 2308.1(3) Å , Z = 8) and a ketoimine (CH3)3CC(NCH3)CH2C(O)C(CH3)3 (3) (space
3
group I41/a, a = 18.7687(6) Å, b = 18.7687(6) Å, c = 14.5182(6) Å, V = 5114.2(3) Å , Z = 16). All
structures are molecular and comprise isolated molecules joined by van der Walls interactions. The
substitution energy of a Na atom for a hydrogen atom in free ligands is calculated by the hybrid B3LYP
quantum chemical method. A successful preparation of Na(I) chelates with ligands 1, 2 and failed attempts
to prepare a complex with ligand 3 are in accordance with the calculations. Geometrical simulation of a
copper(II) complex with ligand 3 reveals the overlap of СН3 groups which hinders the complexation.
Keywords: β-diketones, crystal structure, molecular packing, chelate formation.
Metal complexes of β-diketones and their nitrogen-substituted analogs are volatile, i.e., can be transferred into the
gas phase by moderate heating without decomposing the molecules. Due to this property, metal β-diketonates are widely
applied to obtain metal and oxide coatings (MO CVD [1, 2]). Extended applications facilitated a comprehensive investigation
of these metal complexes, including their structures in the crystalline state, as indicated by CCDC (Cambridge
Crystallographic Data Centre). However, while metal complexes are well represented in CCDC, the structure of the starting
ligands is less studied. Data on the structures of the ligands are necessary to understand both chemical transformations
occurring during the complex formation and processes of thermal destruction of the compounds. The structures of several
A. V. Nikolaev Institute of Inorganic Chemistry, Siberian Division, Russian Academy of Sciences, Novosibirsk;
stabnik@niic.nsc.ru. Translated from Zhurnal Strukturnoi Khimii, Vol. 53, No. 4, pp. 751-757, July-August, 2012. Original
article submitted July 12, 2011; revised November 30, 2011.
740
0022-4766/12/5304-0740

TABLE 1. Structural Data for β-Diketones Studied
Ligand, reference CSD refcode
Year
Space group,
a
c
R
T, K
b, β
Z
Haa [3]
LIWPIQ
LOWPIQ01
YIJYEV
1998
1998
1993
Pnma, 4
Pnma, 4
C2/c, 8
8.396
8.463
15.984
16.031
4.066
4.146
4.81
6.45
3.85
110
210
207
43.396
20.455,
104.27
18.499
[Bi(dpm)3]2⋅Hdpm [4]
NC-dpm [5]
I-dpm [6]
HAKTIX
KUGPUX
2004
1992
1997
P21/c, 4
P21/c, 4
Pbca, 8
9.957
9.188
8.749
20.405,
91.30
5.980
10.628
24.427
5.3
3.9
100
250
283
14.229,
104.74
Hdbm [7]
DBEZLM05
10.840
6.49
β-diketones present in CCDC are given in Table 1 [3-7]. A structural examination has not been carried out for 1,1,1-trifluoro-
4-hydroxy-4-phenyl-but-3-en-2-one (Hbtf, 1), 2,2,6,6-tetramethyl-3-hydroxy-hept-3-en-5-one (Hdpm, 2), and 2,2,6,6-
tetramethyl-3-methylamino-hept-3-en-5-one (Hmi-dpm, 3). This study reports the investigation of the crystal structures of
these ligands, quantum-chemical calculations, and modeling of chelate formation.
EXPERIMENTAL
The Hbtf and Hdpm ligands were purchased from Merck and Dalsib. Hmi-dpm was prepared by amination of Hdpm
with gaseous NH2CH3 in the presence of TiCl4, as described for the synthesis of 2,2,6,6-tetramethyl-3-amino-3-hepten-5-one
(Hi-dpm, 4) in [8]. Hmi-dpm is white powder insoluble in water and soluble in organic solvents. Ligand melting points (hotplate
microscope, °C): 148 (1), 19 (2), 40 (3). C, H, N, F analytical data were obtained on Carlo-Erba 1106 (Italy). For 1 found, %: С
55.5, H 3.2, F 26.4. For С7H7O2F3 calculated, %: С 55.6, H 3.3, F 26.4. For 2 found, %: С 71.8, H 10.8. For С11H20O2 calculated,
%: С 71.7, H 10.9. For 3 found, %: С 73.2, H 11.6, N 7.2. For С12H23ON calculated, %: С 73.0, H 11.8, N 7.1.
IR spectra of the samples were recorded on a Fourier SCIMITAR FTS 2000 spectrophotometer within the range
–1
375-4000 cm in KBr pellets. The resulting spectra are shown in Fig. 1. Selected vibrations for these ligands are:
–1
1 (cm ) νO–H 3493, 3400; νC–H 3122, 3078; νC=O 1617, 1580; νC–F 1312, 1289, 1255; δC–F 773, 900.
–1
2 (cm ) νO–H 3445; νC–H 2967, 2902, 2872; νC=O 1605.
–1
3 (cm ) νO–H 3406; νN–H 3210; νC–H 2964, 2901, 2875; νC=O 1604, 1572; δN–H 1524; νC–N 1203.
–1
4 (cm ) νN–H 3406, 3347, 3175; νC–H 2967, 2907, 2868; νC=O 1633, 1596; δN–H 1525; νC–N 1216.
Interaction of the ligands with sodium metal. The experiments were carried out in dry dioxane. Four test tubes
were loaded with 0.013 g of Na, ∼5 ml of dioxane and ∼ 0.2 g of Hbtf, Hdpm, Hi-dpm, and Hmi-dpm (double excess of the
ligand). Hydrogen evolution was noticed in the tube with Hbtf at room temperature. On heating to 40°C it became observable
also in the tube with Hdpm. On further heating to 80°C the dissolution of sodium accelerated in these tubes, and the reaction
of Na with Hi-dpm became recognizable. No reaction between Na and Hmi-dpm was observed at this temperature. The heating
of the last tube to the dioxane boiling temperature (∼101°C) did not result in the evolution of hydrogen. After heating the tubes
to 80°C for 1 h they were cooled to room temperature. In the tubes with Hbtf and Hdpm, sodium reacted completely. In the tube
with Hi-dpm, sodium was half-dissolved, while in the tube with Hmi-dpm, the weight of sodium did not change.
Interaction of the ligands with Cu(OH) . Freshly prepared Cu(OH)2 was obtained in a water-acetone mixture (1:1)
2
by the reaction of a copper(II) salt with NaOH. The precipitate of Cu(OH)2 was collected on a filter and washed with acetone.
The precipitate was placed in four evaporating dishes, and 0.2 g samples of Hbtf, Hdpm, Hi-dpm, and Hmi-dpm were added
to each of them. (Each of the dishes had a ∼1.5-fold excess of Cu(OH)2.) The expected reaction was
Cu(OH)2 + 2HL → Cu(L)2 + H2O.
741

Fig. 1. IR spectra of the ligands.
TABLE 2. Crystal Data and Experimental Details for Compounds 1, 2, and 3
Compound
Formula
1
2
C11H20O2
184.3
3
C10H7F3O2
216.2
C12H23ON
197.3
Molecular weight
Temperature, K
Wavelength, Å
Crystal system
Space group
150(2)
150(2)
293(2)
0.71073
Monoclinic
P21/c
0.71073
Orthorhombic
Pbca
0.71073
Tetragonal
I41/a
Unit cell parameters
a, b, c, Å; β, deg
7.0713(3), 11.5190(6),
11.3602(6); 99.405(2)
11.5536(8), 11.5796(10),
17.2523(13)
18.7687(6), 18.7687(6),
14.5182(6)
3
V, Å
912.90(8)
4
2308.1(3)
8
5114.2(3)
16
Z
3
dx, g/cm
1.573
1.061
1.025
–1
0.148
0.071
0.064
μ, mm
Crystal size, mm
0.22×0.12×0.06
2.54-27.57
6908
0.34×0.28×0.22
2.36-26.40
15358
0.24×0.20×0.22
3.07-27.11
18850
θ range, deg
I
hkl
measured
2103 [Rint = 0.0191]
1.054
2362 [Rint = 0.0257]
1.068
2808 [Rint = 0.0297]
1.061
I
> 2σ
I
hkl
2
GOOF on F
hkl
R1 = 0.0344, wR2 = 0.0936
R1 = 0.0439, wR2 = 0.0985
R1 = 0.0396, wR2 = 0.1054
R1 = 0.0514, wR2 = 0.1100
R1 = 0.0566, wR2 = 0.1508
R1 = 0.0732, wR2 = 0.1579
R (I > 2σ )
I
R (I msrd.)
hkl
Changes in the color of the reaction mixture indicated the formation of Cu(btf)2 and Cu(dpm)2. No reaction was
observed between Hi-dpm, Hmi-dpm, and Cu(OH)2. However, in one day, dry residue gave evidence of the formation of
Cu(i-dpm)2, but no reaction was observed for Hmi-dpm.
X-ray crystallography. The unit cell parameters and experimental intensity data were measured at 150 K for
C10Н7F3О2 (1), C11Н20О2 (2) and at 293 K for C12Н23ОN (3) on an automated Bruker Nonius X8 Apex diffractometer
equipped with a 4K CCD-detector by the standard method (λMoK , graphite monochromator). Semiempirical absorption
α
correction was applied using the intensities of equivalent reflections (SADABS) [9]. The structures were solved by the direct
2
method and refined by full-matrix least squares against F in the anisotropic approximation for non-hydrogen atoms using
the SHELX97 package [10]. Hydrogen atoms of the organic ligands were set in geometrical positions and refined in the rigid
body approximation. Crystallographic data and experimental details are given in Table 2. Structural data for C10Н7F3О2 (1),
C11Н20О2 (2), and C12Н23ОN (3) have been deposited with CCDC (ССDС 769663, CCDC 755632, CCDC 840627).
742

Fig. 2. Structure of Hbtf (1) (a), Hdpm (2) (b), and Hmi-dpm (3) (c) molecules.
DESCRIPTION OF THE CRYSTAL STRUCTURES
The structures of C10Н7F3О2 (1), C11Н20О2 (2), and C12Н23ОN (3) are built from isolated molecules shown in
Fig. 2a-c respectively. The molecules of ligands 1, 2, and 3, except for the atoms of СF3 and СН3 groups, are practically
planar within 0.06 Å; in ligand 1, deviations of atoms of the Ph ring from the rms plane do not exceed 0.01 Å. In the structure
of 1, the ligand molecules are arranged in layers parallel to the [010] direction (Fig. 3a), while in the structures of compounds
2 and 3 the molecules follow the parquet motif along the а axis (Fig. 3b and c). In the molecule of ligand 3, one of the
С(СН3)3 groups is disordered. Bond lengths are similar in ligands 1, 2, and 3 (Table 3) and match well to the literature data
[11]. Moreover, in the molecules of the ligands there are intramolecular O–H…O (1.735 Å and 1.532 Å for 1 and 2 respectively)
and N–H…O (1.904 Å for 3) hydrogen bonds that form a six-membered planar pseudo- heterocycle (HO2C3) in 1 and 2 and
(HNC3O) in 3. Intermolecular С–H…O contacts (Н…О 2.44 Å) can be noted in the structure of ligand 3 (Fig. 3c).
QUANTUM CHEMICAL CALCULATIONS
Quantum chemical calculations of Hbtf, Hdpm, Hi-dpm, Hmi-dpm and their sodium complexes have been carried out
in order to explain the different reactivity of the ligands in chelate formation. The compounds were calculated at the DFT level
of theory, using Becke’s three-parameter hybrid functional [12] and the Lee-Yang-Parr correlation functional [13] (B3LYP)
implemented in the Jaguar package [14]. Atomic orbitals were described by the 6-31G** basis set. The geometry of the
–4
fragments was optimized analytically to a gradient of 5⋅10 au. Selected bond lengths of the optimized Hbtf, Hdpm, Hi-dpm,
and Hmi-dpm molecules are given in Table 4. Atomic labeling follows the X-ray crystallography notation. The calculated bond
lengths are in good agreement with the experimental values, indicating the applicability of the used quantum chemical approach
for this class of compounds. The analysis of the Table 4 data provides evidence that the О(2)–C(9) bond length is almost
insensitive to the nature of the substituent in the ring and the adjacent chelating atom (oxygen or nitrogen). The C–N bond is
longer than the C–O bond, and the methyl group substitution for the nitrogen hydrogen atom weakens the bond. A successive
elongation of the С(7)–C(8) bond in these series of molecules indicates a decrease in the π-electron interactions between these
743

Fig. 3. Molecular packing in the crystals of Hbtf (a),
Hdpm (b), Hmi-dpm (c).
atoms when the phenyl moiety is substituted by the tert-butyl group, the oxygen atom by nitrogen, and the nitrogen hydrogen
atom by the methyl group. Also in these series, the distance between the carbon atom of the chelate ring and the substituent tends
to enlarge. The C(9)–C(8) distance between the atoms is practically insensible to these substitutions.
form
compl
lig
Na
H
– E – E + E , where E
compl
lig
and E are the
The energy of the complex formation was defined as: E
= E
Na
H
total energies of the complex and the ligand; E and E are the energies of the sodium and hydrogen atoms calculated using
the same basis set as for the compounds. The obtained values are given in Table 4. The positive energy of the complex
formation with sodium indicates the endothermic nature of the process. Therefore, the calculations prove that the complex
744

TABLE 3. Bond Lengths d (Å) for Compounds 1, 2, and 3
Bond
d
Bond
d
Bond
d
Bond
d
Compound 1
Compound 2
C(1)–C(2)
C(1)–C(6)
C(1)–C(7)
C(2)–C(3)
C(3)–C(4)
C(5)–C(4)
C(6)–C(5)
O(1)–C(7)
1.398(2)
1.398(2)
1.470(2)
1.385(2)
1.384(2)
1.390(2)
1.388(2)
1.315(1)
C(8)–C(7)
C(8)–C(9)
O(2)–C(9)
C(9)–C(10)
F(1)–C(10)
F(2)–C(10)
F(3)–C(10)
O(1)–H(1)
1.385(2)
1.406(2)
1.255(2)
1.530(2)
1.331(2)
1.329(2)
1.331(2)
0.882
O(1)–C(1)
O(2)–C(7)
C(1)–C(2)
C(1)–C(6)
C(2)–C(3)
C(2)–C(4)
C(2)–C(5)
1.327(1)
1.256(2)
1.515(2)
1.365(2)
1.533(2)
1.535(2)
1.521(2)
C(7)–C(6)
C(7)–C(8)
C(8)–C(10)
C(8)–C(11)
C(8)–C(9)
O(1)–H(1)
1.434(2)
1.527(2)
1.526(2)
1.527(2)
1.528(2)
1.00
Bond
d
Bond
d
Bond
d
Bond
d
Compound 3
O(1)–C(1)
N(1)–C(2)
N(1)–C(6)
N(1)–H(1)
C(1)–C(3)
1.253(2)
1.339(2)
1.457(2)
0.84(2)
C(1)–C(5)
C(2)–C(3)
C(2)–C(4)
C(3)–H(3)
C(4)–C(43)
1.540(2)
1.392(2)
1.538(2)
0.95(2)
C(4)–C(41)
C(4)–C(42)
C(5)–C(53)
C(5)–C(56)
1.540(3)
1.543(3)
1.393(6)
1.431(13)
C(5)–C(55)
C(5)–C(51)
C(5)–C(54)
C(5)–C(52)
1.475(5)
1.533(7)
1.668(6)
1.669(7)
1.419(2)
1.529(3)
TABLE 4. Bond Lengths (Å) from the B3LYP Calculations of the Molecules and the Interaction Energy of
the Ligands with Sodium (eV)
Bond length
Hbtf
Hdpm
Hi-dpm
Hmi-dpm Bond length
Hbtf
Hdpm
Hi-dpm
Hmi-dpm
O(1)–C(7)
O(2)–C(9)
C(7)–C(8)
C(9)–C(8)
1.318
1.256
1.363
1.453
1.323
1.259
1.380
1.438
—
—
C(7)–C(1)
1.450
1.519
—
1.524
1.542
—
1.539
1.553
1.347
1.25
1.545
1.553
1.352
1.57
1.252
1.385
1.440
1.256
1.395
1.435
C(9)–C(10)
N–C(7)
form
E
of the
0.41
0.75
complex
formation between the ligand and the sodium atom at 0 K is energetically unfavorable. This deficiency should be much
smaller under synthetic conditions (temperature ranging from room to 101°C). An increase in the formation energy of
the sodium complex in the series of the studied ligands is consistent with the experimental trend. Indeed, as we have found,
the formation of the sodium complex is the most rapid with Hbtf; complexation with Hdpm requires more time; the reaction
with Hi-dpm occurs only on heating of the reaction mixture to 80°C, and the complex with Hmi-dpm does not form even in
boiling dioxane.
MODELING OF THE MOLECULAR STRUCTURE OF Cu(mi-dpm)
2
The obtained experimental and theoretical data give evidence that the Hmi-dpm ligand significantly differs from the
other three. Therefore, it needs to explain why ligand 3 does not form Na(I) and Cu(II) chelates. For this purpose, based on
the available structural data for the molecules of Cu(mi-aa)2 [15] and Cu(i-dpm)2 [8], we tried to model the hypothetical
structure of Cu(mi-dpm)2 using the SHELXTL program [9] (Fig. 4a and b). The structure of the chelate cores is different in
these complexes. In Cu(mi-aa)2, metallocylces make an angle of ∼47°, so the nearest environment of the copper atom,
including four oxygen and nitrogen atoms, is intermediate between a square and a tetrahedron (Fig. 4a). The metallocycles
are coplanar in Cu(i-dpm)2, and the nearest environment of the copper atoms is quadratic (Fig. 4c). The task for the
simulation was the replacement of the terminal CH3 groups by (C(CH3)3 groups in the Cu(mi-aa)2 molecule and of the NH
745

Fig. 4. Experimental structure of the Cu(mi-aa)2 molecule (a) and geometrically simulated structure of Cu(mi-
dpm)2 (b). Experimental structure of the Cu(i-dpm)2 molecule (c) and geometrically simulated structure of
Cu(i-dpm)2 (d).
groups by the NCH3 groups in the Cu(i-dpm)2 molecule. All hydrogen atoms of the terminal methyl groups in the Cu(mi-aa)2
molecule were removed and geometrically substituted by six C atoms at a distance of 1.54 Å. Then, hydrogen atoms were
added to these carbon atoms at a distance of 1.0 Å. In the Cu(i-dpm)2 molecule, two hydrogen atoms at the nitrogen atoms
were removed and substituted by C atoms at a distance of 1.45 Å. Hydrogen atoms were added to these carbon atoms at a
distance of 1.0 Å. The structures of the Cu(mi-dpm)2 molecule obtained on transformation of the terminal CH3 groups into
(C(CH3)3 groups in the Cu(mi-aa)2 molecule and on transformation of the NH groups into NCH3 groups in the Cu(i-dpm)2
molecule are shown in Fig. 4b and d. Fig. 4 indicates that the formation of metallocycles for Hmi-dpm must be hindered by
the intraligand overlap of the substituents.
The simulation has shown that the formation of Hmi-dpm metallocycles with Cu(II) should result in the intraligand
overlap of the methyl group atoms at the nitrogen atom and the atoms of one of the methyl groups in the substituent irrespective
of the mutual inclination of the metallocycles. In other words, the formation of the metallocycle is sterically hindered for the
Hmi-dpm ligand, and, hence, the Cu(mi-dpm)2 complex. Similar sterical reasons are likely to explain a failure in the synthesis of
Nami-dpm, in contrast to Naptf, Nadpm, and Nai-dpm in the reaction of metallic sodium with these ligands.
It should be noted that, when this paper was in revision, we succeeded in the preparation of Cu(mi-dpm)2 by the
reaction of ligand 3 with Cu(OCH3)2 in boiling toluene in a stream of dry nitrogen. The complex was purified by sublimation;
Cu(mi-dpm)2 is a green-colored compound; m.p. 152-153°C.
This study was supported by RFBR grant No. 11-03-00197-a.
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746

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