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Glycine hydrogen fluoride: Remarkable hydrogen bonding in the dimeric glycine glycinium cation
Journal of Molecular Structure 984 (2010) 83–88
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Journal of Molecular Structure journal homepage: www.elsevier.com/locate/molstruc
Glycine hydrogen fluoride: Remarkable hydrogen bonding in the dimeric glycine glycinium cation M. Fleck a, V.V. Ghazaryan b, A.M. Petrosyan b,⇑ a b
Institute of Mineralogy and Crystallography, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria Institute of Applied Problems of Physics, NAS of Armenia, 25 Nersessyan Str., 0014 Yerevan, Armenia
a r t i c l e
i n f o
Article history: Received 13 June 2010 Received in revised form 9 September 2010 Accepted 10 September 2010 Available online 17 September 2010 Keywords: Crystal structure Vibrational spectra Salts of amino acids Glycine hydrogen fluoride
a b s t r a c t Crystals of glycine hydrogen fluoride (GlyHF) were prepared from an aqueous solution containing stoichiometric quantities of the components. The crystal structure of GlyHF was determined, IR and Raman spectra were registered and are discussed. GlyHF crystallizes in the orthorhombic space group Pbca with Z = 32. The most remarkable feature of the structure is the existence of symmetric dimeric glycine–glycinium cations with short hydrogen bonds (O O distance of 2.446 Å), charge-counterbalanced by hydrogen bifluoride (FAH F) anions – in addition to the expected glycinium cations and fluoride anions. These results were compared with previously published data on crystals grown in the system glycine– HF–H2O. Ó 2010 Elsevier B.V. All rights reserved.
1. Introduction During our on-going study dealing with the search of new mixed salts of amino acids, we have recently studied the systems glycine + HBF4(HClO4) + H2O and glycine + HF + H2O. The results on the systems glycine + HBF4 + H2O as well as glycine + HClO4 + H2O have already been reported [1], whereas the present paper deals with the system glycine + HF + H2O. This system was studied more than 60 years ago by Frost [2], who prepared diglycine hydrogen chloride (2GlyHCl) as well as the respective bromide and iodide compounds (2GlyHBr and 2GlyHI), and also tried to prepare the likewise fluoride salt (2GlyHF). However, this salt proved elusive as Frost was not able to obtain any such product. Glycine hydrogen fluoride (GlyHF) along with fluorides of other amino acids are used as ingredient of cariostatic compositions [3], although its crystal structure has not been determined up to date. Recently some papers devoted to this system were published. Khandpekar [4] declared that he had succeeded in the growth of diglycine hydrogen fluoride crystal by slow evaporation at room temperature from an aqueous solution with a stoichiometric ratio of components. However, he did not present any physical or chemical data that would have confirmed the composition and structure. In addition, Selvaraju et al. [5] reported the growth of glycine hydrogen fluoride (GlyHF) from an aqueous solution with an equimolar ratio of components by slow evaporation. Again, no ⇑ Corresponding author. Tel.: +374 10 241106; fax: +374 10 281861. E-mail address: [email protected] (A.M. Petrosyan). 0022-2860/$ - see front matter Ó 2010 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2010.09.010
crystal structure was reported, but at least the parameters of an orthorhombic unit cell, an IR spectrum and TG and DTA curves were reported. Moreover, second harmonic generation was detected. The same crystal was obtained and characterized again by Vijayan et al. [6]. Cell parameters, IR spectrum and TG, DTA data are in good agreement with the respective data of [5]. The SHG efficiency measured by the powder technique proved rather high (6.3 times higher than KDP) nonlinear optical activity. However, the results presented in [5,6] do not allow to elucidate the structure of the crystal. (Certainly, the determination of only unit cell dimensions by no means proves composition or structure of any crystal.) In both papers, the authors discussing the IR spectra mention the carboxylate group, which excludes the existence of glycinium cations. Moreover, the IR spectra shown in [5,6] correspond well to the spectrum of a-glycine. Therefore at least for us it remains unclear what crystal species was actually obtained in [5,6]. It is worth to mention also that authors of [7] speaking about diglycine hydrofluoride in their Introduction quoted a reference (N. Vijayan, G. Bhagavannarayana, S. Kumararaman, Mater. Lett. 60 (2006) 2848), which is a strange combination of [5,6]. The papers [5,6], as mentioned above, are devoted to glycine hydrofluoride. Furthermore, they did not quote Ref. [4] in which the 2GlyHF crystal allegedly was obtained. Recently, we emphasized the importance of structure determination of new crystals to avoid such situations [8], and these examples underline this statement. In this contribution we present the results on structure determination and show IR and Raman spectra of glycine hydrogen fluoride, crystallized from an aqueous solution.
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2. Experimental Commercial glycine and hydrofluoric acid (40%, ‘‘Reakhim”, Russia) were used as starting reagents. We had glycine reagent obtained in the Institute of Biotechnology (Yerevan) and reagent of ‘‘Reanal” (Hungary). Both reagents were a-glycine. Since solutions containing hydrofluoric acid react with glass, we used plastic vessels, viz. containers made from polyethylene. Aqueous solutions containing glycine and hydrofluoric acid in molar ratios 2:1, 1:1 and 1:2 were prepared. Salts were obtained by slow evaporation at ambient room temperature. Fourier-transform Raman spectra were registered by a NXP FTRaman Module of a Nicolet 5700 spectrometer (resolution 4 cm1) at room temperature. The same spectrometer was used for measuring attenuated total reflection Fourier-transform infrared spectra (FTIR ATR) (ZnSe prism, 4000–650 cm1, Happ-Genzel apodization, ATR distortion is corrected, number of scans 32, resolution 4 cm1) and FTIR spectra with Nujol mull (4000–400 cm1, number of scans 32, resolution 2 cm1). The single-crystal X-ray intensity data were collected at ambient conditions on a Nonius Kappa CCD-area detector diffractometer. The reflection data were processed with the Nonius program suite Collect [9], and corrected for Lorentz, polarization, background and absorption effects [10]. The crystal structure was determined by direct methods and subsequent Fourier and difference Fourier syntheses, followed by full-matrix leastsquares refinements on F2 [11]. Hydrogen atoms were treated as riding on their parent atoms, with free refinement of the displacement parameters. Scattering factors for neutral atoms were employed in the refinement. The principal crystallographic data and details of structure refinement are shown in Table 1, interatomic distances, angles, and torsion angles are given in Table 2.
3. Results and discussion 3.1. Some notes on the synthesis Because there is some confusion on previous works in the system glycine + HF + H2O, we have tried several attempts to synthesize glycine hydrogen fluoride, in order to find out if another species could be obtained. These include solutions with different molar ratios (as said above). The crystals obtained from the solution with a 2:1 M ratio proved to be c-glycine, identified by their IR spectra [8], while the solutions with the 1:1 and 1:2 M ratios yielded crystals which gave an identical IR spectrum, i.e., one that is different from that of all three glycine polymorphs. The structure determination showed that the composition of these crystals corresponds to a 1:1 M ratio, i.e., the species actually has the composition GlyHF. For the XRD structure determination we used crystals obtained from the solution with a stoichiometric ratio. Furthermore, we have decided to repeat the synthesis of GlyHF crystals from the same solution out of glass vessels. Since hydrofluoric acid readily reacts with the glass, we expected some other species, maybe even some crystals with the unit cell dimensions as given in [5,6].1 The result, however, was neither GlyHF, nor a crystal with the parameters given in [5,6], but the previously known species sodium tris(glycinium) bis(hexafluorosilicate) glycine trisolvate [12]. This confirms the assumption that synthesis of GlyHF is not possible from solutions out of glass containers. 1 Although one assumes that no glass vessels are used for reactions including hydrofluoric acid, there is no clear indication what kind of vessels – glass or plastic – were used in [5,6] for synthesis.
Table 1 Crystallographic data and details of structure refinement of glycine hydrogen fluoride. Formula Mr Crystal size (mm3) Crystal system Space group a (Å) b (Å) c (Å) V (Å3) Z Dcalcd (g cm3) l(Mo Ka) (cm1) F(0 0 0) hkl range T (K) Reflections measured Reflections unique Data with Fo > 4r(Fo) Rint Parameters refined Extinction coefficient R(F)a (for Fo > 4r(Fo)) wR(F2)b (all reflections) Weighting parameters a/b Dqfin(max/min) (e Å3)
C2H6NO2F 95.08 0.04 0.03 0.02 Orthorhombic Pbca 15.610(2) 14.001(2) 15.662(3) 3423.9(9) 32 1.476 0.152 1600 19/23, ±21, ±24 298 33896 6487 4480 0.0264 258 0.0016(7) 0.0422 0.1187 0.052/0.641 0.351/0.210
a
R1 = R||Fo| |Fc||R|Fo|.
b
wR2 = [Rw(F 2o F 2c )2/RwF 4o ]1/2, w = 1/[r2(F 2o )+(a P)2 + b P], P = (F 2o +2F 2c )/3.
Table 2 Intramolecular bond lengths (Å) and angles (°) as well as absolute values of torsion angles (°) in the crystal structure of glycine hydrogen fluoride. Distance/angle
A
B
C
D
O1AC1 O2AC1 C1AC2 C2AN1 O1AC1AO2 O2AC1AC2 O1AC1AC2 C1AC2AN1 O1AC1AC2AN1 O2AC1AC2AN1
1.305(2) 1.210(2) 1.504(2) 1.470(2) 125.5(1) 122.6(1) 112.0(1) 111.3(1) 172.5(1) 7.5(2)
1.311(2) 1.205(2) 1.507(2) 1.469(2) 125.2(1) 123.5(1) 111.3(1) 112.0(1) 175.2(1) 5.3(2)
1.315(2) 1.209(2) 1.504(2) 1.470(2) 125.6(1) 122.5(1) 111.8(1) 110.45(9) 175.1(1) 5.1(2)
1.292(1) 1.219(1) 1.511(1) 1.474(1) 125.6(1) 121.18(9) 113.22(9) 110.43(9) 176.9(1) 3.3(2)
3.2. Crystal and molecular structure of glycine hydrogen fluoride The title compound was found to crystallize in the orthorhombic system in the centrosymmetric space group Pbca with four crystallographically independent moieties. The molecular structure with labeling of the atoms is shown in Fig. 1. Closer examination of the packing (see packing diagram in Fig. 2) and the hydrogen bond network (Table 3) reveals some unexpected, interesting features of the structure. Three glycinium cations, namely, Gly(A), Gly(B), Gly(C) form strong OAHF type hydrogen bonds with the F(1), F(2), and F(3) fluoride anions, respectively (O F distances 2.436 Å, 2.476 Å, and 2.446 Å). In addition, these fluoride anions act as acceptors to each three NAH F type hydrogen bonds. Thus, each of these three fluoride anions has one oxygen atom and three nitrogen atoms in their environments. The remaining glycinium cation and fluoride anion, viz. Gly(D) and F4, have quite a different environment. This was puzzling at first because of some trouble with one hydrogen atom, namely the acid hydrogen of moiety Gly(D), H1D. As it turned out, this molecule is symmetry related with itself via an inversion center, about which the hydrogen bond is located (Fig. 3a). This means the hydrogen position cannot be fully occupied, but must be half-occupied, i.e. disordered about the two symmetry-equivalent positions. In this case
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M. Fleck et al. / Journal of Molecular Structure 984 (2010) 83–88 Table 3 Hydrogen bond parameters (in Å and °) for glycine hydrogen fluoride.
O2A
C2A
F1
C1A
N1A
O1A
O2D
N1D
C1D
C2D
O1D
F4
F3
N1B O1C C2B O1B O2B
C1C
DAH A
d(DAH)
d(H A)
d(D A)
DHA
O1DAH1D O1D N1DAH11D F3 N1DAH12D F4 N1DAH13D F1 O1AAH1A F1 N1AAH11A F4 N1AAH12A F1 N1AAH13A F2 O1BAH1B F2 N1BAH11B F3 N1BAH12B F2 N1BAH13B O1D O1CAH1C F3 N1CAH11C F1 N1CAH12C F3 N1CAH13C F2 F4AH4 F4
0.93(2) 0.89 0.89 0.89 0.99(2) 0.89 0.89 0.89 0.98(2) 0.89 0.89 0.89 0.99(2) 0.89 0.89 0.89 0.97(2)
1.53(2) 1.96 1.89 1.96 1.45(2) 1.92 1.80 1.86 1.50(2) 1.83 1.84 2.02 1.45(2) 1.95 1.76 1.85 1.32(2)
2.446(2) 2.837(1) 2.727(1) 2.847(1) 2.436(1) 2.799(1) 2.680(1) 2.742(1) 2.476(1) 2.721(1) 2.719(1) 2.902(1) 2.446(1) 2.8289(1) 2.644(1) 2.737(1) 2.267(2)
167(4) 166.4 156.4 171.5 176(2) 169.7 169.5 169.4 171(2) 173.9 170.0 172.9 178(2) 169.1 175.0 172.8 163(6)
O2C
C1B C2C N1C F2
Fig. 1. Molecular structure and atom labeling in glycine hydrogen fluoride. For the symmetry-related pairs of [Gly(D) H Gly(D)] and [F(4) H F(4)] the related counterpart is shown (see text).
Fig. 2. Packing diagram of glycine hydrogen fluoride, viewed along [1 0 0]. Hydrogen atoms are omitted for clarity.
of the inversion center between the symmetry-related pair of F4 atoms (so-called hydrogen bifluoride anions (FAH F), with F F distances equal to 2.267 Å). From further refinement, it was found that this hydrogen atom is located off-center as well, also half-occupied and disordered (Fig. 3b). Since we supposed that the symmetry might be incorrect and that the structure could in fact be of a lower symmetry without any disorder, we also tried refinement in the subgroup P212121. Here we found exactly the same atomic arrangement, including the half-occupied, disordered hydrogen atoms H4 and H1D, and certainly checking routines indicated that the structure is in fact centrosymmetric, space group Pbca. To be sure, we made a quick powder SHG test, which gave no activity whatsoever. Of course, the absence of SHG is no proof for centrosymmetry, but it does support the centrosymmetric structure model. Both donor/acceptor atoms of the half-occupied hydrogen atoms differs from the respective atoms of the other moieties in another way: The O1D atom, on one hand, additionally acts as acceptor for another hydrogen bond extending from nitrogen N1B (see Table 3). The F4 atom, on the other hand, differs from the other fluoride anions by that in addition to the FAH F hydrogen bond, it participates in only two hydrogen bonds, namely from the cations Gly(A) and Gly(D), via NAH F type hydrogen bonds (Table 3), with an N1AAF4AN1Dangle equal to 112°. All CAN and C1AC2 bond lengths in all glycine moieties are similar to each other (and to the usual values), while the C1DAO1 and C1DAO2 distances are somewhat shorter and longer than the respective bonds in three other glycine moieties due to the strong hydrogen bond in hydrogen diglycine cation (Table 2). 3.3. Vibrational spectra of glycine hydrogen fluoride
we have a symmetric hydrogen diglycine cation (Gly H Gly)+, with a strong O O hydrogen bond equal to 2.446 Å. Consequently, we found that the negative charge from the fluorine ions is not fully counterbalanced. Therefore, we looked through the residual electron density and located another hydrogen atom in proximity
In addition to the single crystal data, we have recorded IR and Raman spectra of glycine hydrogen fluoride (Fig. 4). In these spectra we expected to find vibrations typical for glycinium cations, glycine glycinium dimeric cations, and hydrogen bifluoride anions.
Fig. 3. Details of the hydrogen bonds including the half-occupied, disordered hydrogen atoms H1D (a) and H4 (b).
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Fig. 4. IR (ATR (a), Nujol mull (b)) and Raman spectra of glycine hydrogen fluoride. Asterisks show absorption bands of Nujol.
Some considerations of the vibrations of the glycinium cation can be found in [13–17]. In the high-frequency region of the Raman spectrum (Fig. 4) one can see intensive lines characteristic for stretching vibration of CAH bonds with peaks at 3020 cm1, 3002 cm1, 2982 cm1 and a shoulder at 2973 cm1. These intensive lines overlap with a broad band in the region ca. 3350–2600 cm1, which we assign to stretching vibrations of NAH bonds participating in various hydrogen bonds. In the IR spectrum, the stretching vibrations of NAH bonds are usually stronger than the stretching vibrations of
CAH bonds. In the same (3350–2600 cm1) region of the IR spectrum one can see respective peaks caused by stretching vibration of CAH bonds at 3020 cm1, 3002 cm1, 2979 cm1, and 2957 cm1, overlapped with a broad band with peaks at 2883 cm1, 2849 cm1, 2758 cm1, 2665 cm1, which we assign to stretching vibrations of NAH bonds. Their positions agree well with the known correlation of m(NH) versus N F distance [18]. Absorption bands in the region 2600–2000 cm1 we assign to sum tones, since this region of wavenumbers – according to the correlation from [18] – is lower than the value of m(NH) expected
M. Fleck et al. / Journal of Molecular Structure 984 (2010) 83–88
for the shortest NAH F hydrogen bond, viz. 2.644 Å for N1CAH F3, and at the same time is higher than that expected for m(OH) [18,19] in the short hydrogen bond of the glycine glycinium dimer. In addition, the almost full absence of scattering lines in the Raman spectrum in this region supports our assessment. The band at 1953 cm1 may be caused by m(FH). Its position agrees with the m(FH) versus FAH F correlation [18]. In the region expected for m(C@O) in glycinium cations we find peaks at 1753 cm1 and 1717 cm1 in the IR spectrum. Because of the weakness of the peak at 1753 cm1 and the almost complete absence of its counterpart in the Raman spectrum, we could not rule out the possibility that this peak is an overtone. In the Raman spectrum, in addition to the peaks at 1725 cm1 and 1713 cm1, there is a peak at 1685 cm1, which has no counterpart in the IR spectrum. We believe that this peak is caused by m(C@O) of the glycine glycinium dimer. The absence of the IR counterpart may be caused by the presence of the inversion center in the hydrogen diglycine dimeric cation. The strong absorption band at 1277 cm1 and the shoulder at 1264 cm1 we assign to m(CAOH). However, we find it difficult to identify the absorption caused by m(OH) in the hydrogen diglycine dimeric cation because of presence additionally the rather strong OAH F hydrogen bonds. The presence of very broad absorption in the region between 2000 and 400 cm1 caused by m(OH) of OAH F and O H O hydrogen bonds can be better seen in the IR spectrum registered with Nujol mull. Assessments of other bands are shown in Table 4. The peaks at 681, 660, 580 and 529 cm1 may be assigned to deformation vibrations of COOH and COO groups (following [17]). During the study of glycinium fluoride by Raman spectroscopy we made another interesting observation, which may additionally elucidate the issue of the ‘‘observation of second harmonic generation in centrosymmetric crystals” as commented on in [8]. After the registration of Raman spectra from powdered samples of glycinium fluoride we decided to improve the quality of the spectra and registered the spectrum after some time from the same sample. To
Table 4 Wavenumbers and assignment in the IR and Raman spectra of glycine hydrogen fluoride. IR 3020; 3002 2979; 2957 2883; 2849 2758 2665 2551 2466; 2379 2197 1953; 1910sh 1753; 1717 1651sh; 1621 1543 1465; 1434 1394 1312 1277; 1264sh 1202 1176; 1141 1121 1081; 1051; 1040 931; 923 885; 877 811 654 571 528; 512sh
Raman
Assessment
3118; 3020; 2982; 2858 2780; 2677;
m(NH) NHþ3 m(CH) CH2, m(CH) CH2 m(NH) NHþ3 m(NH) NHþ3 m(NH) NHþ3
3094; 3075 3002 2973sh 2766 2658
1725; 1713; 1685 1644 1461; 1436;1423sh 1399 1326sh; 1317 1282; 1259 1165; 1140 1053 926 905; 886 681; 660 580 529 354; 332; 305; 242; 222
Sum tone Sum tone Sum tone m(FH) m(C@O) das(NH3+) ds(NH3+) d(CH2)
x(CH2) m(CAOH)
q(NH3+) q(NH3+) m(CAN) q(CH2) m(CAC)
87
our great surprise the powdered sample of glycinium fluoride had turned into the c-glycine, while the initial non-powdered sample remained unchanged. It is known that c-glycine in contrast to aglycine is non-centrosymmetrical and therefore nonlinear optically active. We assume that this same effect may be responsible for the detection of SHG signals in various centrosymmetrical crystals (see [8] and Refs. therein). Moreover, later we noted that the surface of large transparent crystals of GlyHF in usual laboratory condition in time become nontransparent. IR spectrum of scraped nontransparent layer showed that it represents c-glycine. 4. Conclusions We have shown that glycine hydrogen fluoride crystals can be synthesized and grown from an aqueous solution of equimolar quantities of glycine and hydrofluoric acid by means of the slow evaporation technique, using plastic vessels. It has also been shown that the same reaction in glass vessels does not yield glycine hydrogen fluoride, instead a reaction with the glass produces sodium tris(glycinium) bis(hexafluorosilicate) glycine trisolvate [12]. Glycine hydrogen fluoride has been structurally and spectroscopically characterized. It crystallizes in an orthorhombic centrosymmetric structure (space group Pbca) and comprises three glycinium cations, three fluoride anions and also symmetric hydrogen diglycine cation and hydrogen bifluoride anion. Furthermore, we have made an interesting observation that this species, when ground to powder and left alone for a couple of weeks, turns at least partially into c-glycine. This fact is more important that it seems, because recently many papers have reported SHG activity in centrosymmetrical glycine compounds (see [8] and Refs. therein), an effect physically impossible. We think that in these cases a likewise transition had occurred, yielding non-centrosymmetrical c-glycine, responsible for the reported SHG signals. Moreover, later we noted that the surface of large transparent crystals of GlyHF in usual laboratory condition in time become nontransparent. The IR spectrum of scraped nontransparent layer showed that it represents c-glycine. 5. Supplementary material Supplementary crystallographic data for this paper have been deposited. These data can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retrieving.html (or from the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 36033), quoting this paper and the CCDC Number 779604. Acknowledgment This work was made possible by the research Grant PS1839 from the Armenian National Science and Education Fund (ANSEF) based in New York, USA. References [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]
V.V. Ghazaryan, M. Fleck, A.M. Petrosyan, J. Mol. Struct. 977 (2010) 117–129. W.S. Frost, J. Am. Chem. Soc. 64 (1942) 1286–1287. H. Schmid, US Patent # 3413,326, 1968. M.M. Khandpekar, Indian J. Pure Appl. Phys. 41 (2003) 704–706. K. Selvaraju, R. Valluvan, S. Kumararaman, Mater. Lett. 60 (2006) 2848–2850. N. Vijayan, G. Bhagavannarayana, S.N. Sharma, J. Mater. Sci. 44 (2009) 3457– 3461. M.M. Khandpekar, S.P. Pati, J. Cryst. Growth 312 (2010) 1150–1153. M. Fleck, A.M. Petrosyan, J. Cryst. Growth 312 (2010) 2284–2290. Nonius, Collect, Nonius BV, Delft (The Netherlands), 2003. Z. Otwinowski, W. Minor, Methods Enzymol. Part A 276 (1997) 307–326. G.M. Sheldrick, Acta Crystallogr. A64 (2008) 112–122. M.B. Narayana, C. Rai, S.M. Dharmaprakash, W.T.A. Harrison, Acta Crystallogr. C63 (2007) m312–m314.
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[18] K. Nakamoto, M. Margoshes, R.E. Rundle, J. Am. Chem. Soc. 77 (1955) 6480– 6486. [19] A. Novak, in: Infrared and Raman Spectroscopy of Biological Molecules, Proc. NATO Advanced Study Institute, Athens, August 22–31, 1978. Dordrecht, 1979, pp. 279–303.
Contents lists available at ScienceDirect
Journal of Molecular Structure journal homepage: www.elsevier.com/locate/molstruc
Glycine hydrogen fluoride: Remarkable hydrogen bonding in the dimeric glycine glycinium cation M. Fleck a, V.V. Ghazaryan b, A.M. Petrosyan b,⇑ a b
Institute of Mineralogy and Crystallography, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria Institute of Applied Problems of Physics, NAS of Armenia, 25 Nersessyan Str., 0014 Yerevan, Armenia
a r t i c l e
i n f o
Article history: Received 13 June 2010 Received in revised form 9 September 2010 Accepted 10 September 2010 Available online 17 September 2010 Keywords: Crystal structure Vibrational spectra Salts of amino acids Glycine hydrogen fluoride
a b s t r a c t Crystals of glycine hydrogen fluoride (GlyHF) were prepared from an aqueous solution containing stoichiometric quantities of the components. The crystal structure of GlyHF was determined, IR and Raman spectra were registered and are discussed. GlyHF crystallizes in the orthorhombic space group Pbca with Z = 32. The most remarkable feature of the structure is the existence of symmetric dimeric glycine–glycinium cations with short hydrogen bonds (O O distance of 2.446 Å), charge-counterbalanced by hydrogen bifluoride (FAH F) anions – in addition to the expected glycinium cations and fluoride anions. These results were compared with previously published data on crystals grown in the system glycine– HF–H2O. Ó 2010 Elsevier B.V. All rights reserved.
1. Introduction During our on-going study dealing with the search of new mixed salts of amino acids, we have recently studied the systems glycine + HBF4(HClO4) + H2O and glycine + HF + H2O. The results on the systems glycine + HBF4 + H2O as well as glycine + HClO4 + H2O have already been reported [1], whereas the present paper deals with the system glycine + HF + H2O. This system was studied more than 60 years ago by Frost [2], who prepared diglycine hydrogen chloride (2GlyHCl) as well as the respective bromide and iodide compounds (2GlyHBr and 2GlyHI), and also tried to prepare the likewise fluoride salt (2GlyHF). However, this salt proved elusive as Frost was not able to obtain any such product. Glycine hydrogen fluoride (GlyHF) along with fluorides of other amino acids are used as ingredient of cariostatic compositions [3], although its crystal structure has not been determined up to date. Recently some papers devoted to this system were published. Khandpekar [4] declared that he had succeeded in the growth of diglycine hydrogen fluoride crystal by slow evaporation at room temperature from an aqueous solution with a stoichiometric ratio of components. However, he did not present any physical or chemical data that would have confirmed the composition and structure. In addition, Selvaraju et al. [5] reported the growth of glycine hydrogen fluoride (GlyHF) from an aqueous solution with an equimolar ratio of components by slow evaporation. Again, no ⇑ Corresponding author. Tel.: +374 10 241106; fax: +374 10 281861. E-mail address: [email protected] (A.M. Petrosyan). 0022-2860/$ - see front matter Ó 2010 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2010.09.010
crystal structure was reported, but at least the parameters of an orthorhombic unit cell, an IR spectrum and TG and DTA curves were reported. Moreover, second harmonic generation was detected. The same crystal was obtained and characterized again by Vijayan et al. [6]. Cell parameters, IR spectrum and TG, DTA data are in good agreement with the respective data of [5]. The SHG efficiency measured by the powder technique proved rather high (6.3 times higher than KDP) nonlinear optical activity. However, the results presented in [5,6] do not allow to elucidate the structure of the crystal. (Certainly, the determination of only unit cell dimensions by no means proves composition or structure of any crystal.) In both papers, the authors discussing the IR spectra mention the carboxylate group, which excludes the existence of glycinium cations. Moreover, the IR spectra shown in [5,6] correspond well to the spectrum of a-glycine. Therefore at least for us it remains unclear what crystal species was actually obtained in [5,6]. It is worth to mention also that authors of [7] speaking about diglycine hydrofluoride in their Introduction quoted a reference (N. Vijayan, G. Bhagavannarayana, S. Kumararaman, Mater. Lett. 60 (2006) 2848), which is a strange combination of [5,6]. The papers [5,6], as mentioned above, are devoted to glycine hydrofluoride. Furthermore, they did not quote Ref. [4] in which the 2GlyHF crystal allegedly was obtained. Recently, we emphasized the importance of structure determination of new crystals to avoid such situations [8], and these examples underline this statement. In this contribution we present the results on structure determination and show IR and Raman spectra of glycine hydrogen fluoride, crystallized from an aqueous solution.
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2. Experimental Commercial glycine and hydrofluoric acid (40%, ‘‘Reakhim”, Russia) were used as starting reagents. We had glycine reagent obtained in the Institute of Biotechnology (Yerevan) and reagent of ‘‘Reanal” (Hungary). Both reagents were a-glycine. Since solutions containing hydrofluoric acid react with glass, we used plastic vessels, viz. containers made from polyethylene. Aqueous solutions containing glycine and hydrofluoric acid in molar ratios 2:1, 1:1 and 1:2 were prepared. Salts were obtained by slow evaporation at ambient room temperature. Fourier-transform Raman spectra were registered by a NXP FTRaman Module of a Nicolet 5700 spectrometer (resolution 4 cm1) at room temperature. The same spectrometer was used for measuring attenuated total reflection Fourier-transform infrared spectra (FTIR ATR) (ZnSe prism, 4000–650 cm1, Happ-Genzel apodization, ATR distortion is corrected, number of scans 32, resolution 4 cm1) and FTIR spectra with Nujol mull (4000–400 cm1, number of scans 32, resolution 2 cm1). The single-crystal X-ray intensity data were collected at ambient conditions on a Nonius Kappa CCD-area detector diffractometer. The reflection data were processed with the Nonius program suite Collect [9], and corrected for Lorentz, polarization, background and absorption effects [10]. The crystal structure was determined by direct methods and subsequent Fourier and difference Fourier syntheses, followed by full-matrix leastsquares refinements on F2 [11]. Hydrogen atoms were treated as riding on their parent atoms, with free refinement of the displacement parameters. Scattering factors for neutral atoms were employed in the refinement. The principal crystallographic data and details of structure refinement are shown in Table 1, interatomic distances, angles, and torsion angles are given in Table 2.
3. Results and discussion 3.1. Some notes on the synthesis Because there is some confusion on previous works in the system glycine + HF + H2O, we have tried several attempts to synthesize glycine hydrogen fluoride, in order to find out if another species could be obtained. These include solutions with different molar ratios (as said above). The crystals obtained from the solution with a 2:1 M ratio proved to be c-glycine, identified by their IR spectra [8], while the solutions with the 1:1 and 1:2 M ratios yielded crystals which gave an identical IR spectrum, i.e., one that is different from that of all three glycine polymorphs. The structure determination showed that the composition of these crystals corresponds to a 1:1 M ratio, i.e., the species actually has the composition GlyHF. For the XRD structure determination we used crystals obtained from the solution with a stoichiometric ratio. Furthermore, we have decided to repeat the synthesis of GlyHF crystals from the same solution out of glass vessels. Since hydrofluoric acid readily reacts with the glass, we expected some other species, maybe even some crystals with the unit cell dimensions as given in [5,6].1 The result, however, was neither GlyHF, nor a crystal with the parameters given in [5,6], but the previously known species sodium tris(glycinium) bis(hexafluorosilicate) glycine trisolvate [12]. This confirms the assumption that synthesis of GlyHF is not possible from solutions out of glass containers. 1 Although one assumes that no glass vessels are used for reactions including hydrofluoric acid, there is no clear indication what kind of vessels – glass or plastic – were used in [5,6] for synthesis.
Table 1 Crystallographic data and details of structure refinement of glycine hydrogen fluoride. Formula Mr Crystal size (mm3) Crystal system Space group a (Å) b (Å) c (Å) V (Å3) Z Dcalcd (g cm3) l(Mo Ka) (cm1) F(0 0 0) hkl range T (K) Reflections measured Reflections unique Data with Fo > 4r(Fo) Rint Parameters refined Extinction coefficient R(F)a (for Fo > 4r(Fo)) wR(F2)b (all reflections) Weighting parameters a/b Dqfin(max/min) (e Å3)
C2H6NO2F 95.08 0.04 0.03 0.02 Orthorhombic Pbca 15.610(2) 14.001(2) 15.662(3) 3423.9(9) 32 1.476 0.152 1600 19/23, ±21, ±24 298 33896 6487 4480 0.0264 258 0.0016(7) 0.0422 0.1187 0.052/0.641 0.351/0.210
a
R1 = R||Fo| |Fc||R|Fo|.
b
wR2 = [Rw(F 2o F 2c )2/RwF 4o ]1/2, w = 1/[r2(F 2o )+(a P)2 + b P], P = (F 2o +2F 2c )/3.
Table 2 Intramolecular bond lengths (Å) and angles (°) as well as absolute values of torsion angles (°) in the crystal structure of glycine hydrogen fluoride. Distance/angle
A
B
C
D
O1AC1 O2AC1 C1AC2 C2AN1 O1AC1AO2 O2AC1AC2 O1AC1AC2 C1AC2AN1 O1AC1AC2AN1 O2AC1AC2AN1
1.305(2) 1.210(2) 1.504(2) 1.470(2) 125.5(1) 122.6(1) 112.0(1) 111.3(1) 172.5(1) 7.5(2)
1.311(2) 1.205(2) 1.507(2) 1.469(2) 125.2(1) 123.5(1) 111.3(1) 112.0(1) 175.2(1) 5.3(2)
1.315(2) 1.209(2) 1.504(2) 1.470(2) 125.6(1) 122.5(1) 111.8(1) 110.45(9) 175.1(1) 5.1(2)
1.292(1) 1.219(1) 1.511(1) 1.474(1) 125.6(1) 121.18(9) 113.22(9) 110.43(9) 176.9(1) 3.3(2)
3.2. Crystal and molecular structure of glycine hydrogen fluoride The title compound was found to crystallize in the orthorhombic system in the centrosymmetric space group Pbca with four crystallographically independent moieties. The molecular structure with labeling of the atoms is shown in Fig. 1. Closer examination of the packing (see packing diagram in Fig. 2) and the hydrogen bond network (Table 3) reveals some unexpected, interesting features of the structure. Three glycinium cations, namely, Gly(A), Gly(B), Gly(C) form strong OAHF type hydrogen bonds with the F(1), F(2), and F(3) fluoride anions, respectively (O F distances 2.436 Å, 2.476 Å, and 2.446 Å). In addition, these fluoride anions act as acceptors to each three NAH F type hydrogen bonds. Thus, each of these three fluoride anions has one oxygen atom and three nitrogen atoms in their environments. The remaining glycinium cation and fluoride anion, viz. Gly(D) and F4, have quite a different environment. This was puzzling at first because of some trouble with one hydrogen atom, namely the acid hydrogen of moiety Gly(D), H1D. As it turned out, this molecule is symmetry related with itself via an inversion center, about which the hydrogen bond is located (Fig. 3a). This means the hydrogen position cannot be fully occupied, but must be half-occupied, i.e. disordered about the two symmetry-equivalent positions. In this case
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M. Fleck et al. / Journal of Molecular Structure 984 (2010) 83–88 Table 3 Hydrogen bond parameters (in Å and °) for glycine hydrogen fluoride.
O2A
C2A
F1
C1A
N1A
O1A
O2D
N1D
C1D
C2D
O1D
F4
F3
N1B O1C C2B O1B O2B
C1C
DAH A
d(DAH)
d(H A)
d(D A)
DHA
O1DAH1D O1D N1DAH11D F3 N1DAH12D F4 N1DAH13D F1 O1AAH1A F1 N1AAH11A F4 N1AAH12A F1 N1AAH13A F2 O1BAH1B F2 N1BAH11B F3 N1BAH12B F2 N1BAH13B O1D O1CAH1C F3 N1CAH11C F1 N1CAH12C F3 N1CAH13C F2 F4AH4 F4
0.93(2) 0.89 0.89 0.89 0.99(2) 0.89 0.89 0.89 0.98(2) 0.89 0.89 0.89 0.99(2) 0.89 0.89 0.89 0.97(2)
1.53(2) 1.96 1.89 1.96 1.45(2) 1.92 1.80 1.86 1.50(2) 1.83 1.84 2.02 1.45(2) 1.95 1.76 1.85 1.32(2)
2.446(2) 2.837(1) 2.727(1) 2.847(1) 2.436(1) 2.799(1) 2.680(1) 2.742(1) 2.476(1) 2.721(1) 2.719(1) 2.902(1) 2.446(1) 2.8289(1) 2.644(1) 2.737(1) 2.267(2)
167(4) 166.4 156.4 171.5 176(2) 169.7 169.5 169.4 171(2) 173.9 170.0 172.9 178(2) 169.1 175.0 172.8 163(6)
O2C
C1B C2C N1C F2
Fig. 1. Molecular structure and atom labeling in glycine hydrogen fluoride. For the symmetry-related pairs of [Gly(D) H Gly(D)] and [F(4) H F(4)] the related counterpart is shown (see text).
Fig. 2. Packing diagram of glycine hydrogen fluoride, viewed along [1 0 0]. Hydrogen atoms are omitted for clarity.
of the inversion center between the symmetry-related pair of F4 atoms (so-called hydrogen bifluoride anions (FAH F), with F F distances equal to 2.267 Å). From further refinement, it was found that this hydrogen atom is located off-center as well, also half-occupied and disordered (Fig. 3b). Since we supposed that the symmetry might be incorrect and that the structure could in fact be of a lower symmetry without any disorder, we also tried refinement in the subgroup P212121. Here we found exactly the same atomic arrangement, including the half-occupied, disordered hydrogen atoms H4 and H1D, and certainly checking routines indicated that the structure is in fact centrosymmetric, space group Pbca. To be sure, we made a quick powder SHG test, which gave no activity whatsoever. Of course, the absence of SHG is no proof for centrosymmetry, but it does support the centrosymmetric structure model. Both donor/acceptor atoms of the half-occupied hydrogen atoms differs from the respective atoms of the other moieties in another way: The O1D atom, on one hand, additionally acts as acceptor for another hydrogen bond extending from nitrogen N1B (see Table 3). The F4 atom, on the other hand, differs from the other fluoride anions by that in addition to the FAH F hydrogen bond, it participates in only two hydrogen bonds, namely from the cations Gly(A) and Gly(D), via NAH F type hydrogen bonds (Table 3), with an N1AAF4AN1Dangle equal to 112°. All CAN and C1AC2 bond lengths in all glycine moieties are similar to each other (and to the usual values), while the C1DAO1 and C1DAO2 distances are somewhat shorter and longer than the respective bonds in three other glycine moieties due to the strong hydrogen bond in hydrogen diglycine cation (Table 2). 3.3. Vibrational spectra of glycine hydrogen fluoride
we have a symmetric hydrogen diglycine cation (Gly H Gly)+, with a strong O O hydrogen bond equal to 2.446 Å. Consequently, we found that the negative charge from the fluorine ions is not fully counterbalanced. Therefore, we looked through the residual electron density and located another hydrogen atom in proximity
In addition to the single crystal data, we have recorded IR and Raman spectra of glycine hydrogen fluoride (Fig. 4). In these spectra we expected to find vibrations typical for glycinium cations, glycine glycinium dimeric cations, and hydrogen bifluoride anions.
Fig. 3. Details of the hydrogen bonds including the half-occupied, disordered hydrogen atoms H1D (a) and H4 (b).
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Fig. 4. IR (ATR (a), Nujol mull (b)) and Raman spectra of glycine hydrogen fluoride. Asterisks show absorption bands of Nujol.
Some considerations of the vibrations of the glycinium cation can be found in [13–17]. In the high-frequency region of the Raman spectrum (Fig. 4) one can see intensive lines characteristic for stretching vibration of CAH bonds with peaks at 3020 cm1, 3002 cm1, 2982 cm1 and a shoulder at 2973 cm1. These intensive lines overlap with a broad band in the region ca. 3350–2600 cm1, which we assign to stretching vibrations of NAH bonds participating in various hydrogen bonds. In the IR spectrum, the stretching vibrations of NAH bonds are usually stronger than the stretching vibrations of
CAH bonds. In the same (3350–2600 cm1) region of the IR spectrum one can see respective peaks caused by stretching vibration of CAH bonds at 3020 cm1, 3002 cm1, 2979 cm1, and 2957 cm1, overlapped with a broad band with peaks at 2883 cm1, 2849 cm1, 2758 cm1, 2665 cm1, which we assign to stretching vibrations of NAH bonds. Their positions agree well with the known correlation of m(NH) versus N F distance [18]. Absorption bands in the region 2600–2000 cm1 we assign to sum tones, since this region of wavenumbers – according to the correlation from [18] – is lower than the value of m(NH) expected
M. Fleck et al. / Journal of Molecular Structure 984 (2010) 83–88
for the shortest NAH F hydrogen bond, viz. 2.644 Å for N1CAH F3, and at the same time is higher than that expected for m(OH) [18,19] in the short hydrogen bond of the glycine glycinium dimer. In addition, the almost full absence of scattering lines in the Raman spectrum in this region supports our assessment. The band at 1953 cm1 may be caused by m(FH). Its position agrees with the m(FH) versus FAH F correlation [18]. In the region expected for m(C@O) in glycinium cations we find peaks at 1753 cm1 and 1717 cm1 in the IR spectrum. Because of the weakness of the peak at 1753 cm1 and the almost complete absence of its counterpart in the Raman spectrum, we could not rule out the possibility that this peak is an overtone. In the Raman spectrum, in addition to the peaks at 1725 cm1 and 1713 cm1, there is a peak at 1685 cm1, which has no counterpart in the IR spectrum. We believe that this peak is caused by m(C@O) of the glycine glycinium dimer. The absence of the IR counterpart may be caused by the presence of the inversion center in the hydrogen diglycine dimeric cation. The strong absorption band at 1277 cm1 and the shoulder at 1264 cm1 we assign to m(CAOH). However, we find it difficult to identify the absorption caused by m(OH) in the hydrogen diglycine dimeric cation because of presence additionally the rather strong OAH F hydrogen bonds. The presence of very broad absorption in the region between 2000 and 400 cm1 caused by m(OH) of OAH F and O H O hydrogen bonds can be better seen in the IR spectrum registered with Nujol mull. Assessments of other bands are shown in Table 4. The peaks at 681, 660, 580 and 529 cm1 may be assigned to deformation vibrations of COOH and COO groups (following [17]). During the study of glycinium fluoride by Raman spectroscopy we made another interesting observation, which may additionally elucidate the issue of the ‘‘observation of second harmonic generation in centrosymmetric crystals” as commented on in [8]. After the registration of Raman spectra from powdered samples of glycinium fluoride we decided to improve the quality of the spectra and registered the spectrum after some time from the same sample. To
Table 4 Wavenumbers and assignment in the IR and Raman spectra of glycine hydrogen fluoride. IR 3020; 3002 2979; 2957 2883; 2849 2758 2665 2551 2466; 2379 2197 1953; 1910sh 1753; 1717 1651sh; 1621 1543 1465; 1434 1394 1312 1277; 1264sh 1202 1176; 1141 1121 1081; 1051; 1040 931; 923 885; 877 811 654 571 528; 512sh
Raman
Assessment
3118; 3020; 2982; 2858 2780; 2677;
m(NH) NHþ3 m(CH) CH2, m(CH) CH2 m(NH) NHþ3 m(NH) NHþ3 m(NH) NHþ3
3094; 3075 3002 2973sh 2766 2658
1725; 1713; 1685 1644 1461; 1436;1423sh 1399 1326sh; 1317 1282; 1259 1165; 1140 1053 926 905; 886 681; 660 580 529 354; 332; 305; 242; 222
Sum tone Sum tone Sum tone m(FH) m(C@O) das(NH3+) ds(NH3+) d(CH2)
x(CH2) m(CAOH)
q(NH3+) q(NH3+) m(CAN) q(CH2) m(CAC)
87
our great surprise the powdered sample of glycinium fluoride had turned into the c-glycine, while the initial non-powdered sample remained unchanged. It is known that c-glycine in contrast to aglycine is non-centrosymmetrical and therefore nonlinear optically active. We assume that this same effect may be responsible for the detection of SHG signals in various centrosymmetrical crystals (see [8] and Refs. therein). Moreover, later we noted that the surface of large transparent crystals of GlyHF in usual laboratory condition in time become nontransparent. IR spectrum of scraped nontransparent layer showed that it represents c-glycine. 4. Conclusions We have shown that glycine hydrogen fluoride crystals can be synthesized and grown from an aqueous solution of equimolar quantities of glycine and hydrofluoric acid by means of the slow evaporation technique, using plastic vessels. It has also been shown that the same reaction in glass vessels does not yield glycine hydrogen fluoride, instead a reaction with the glass produces sodium tris(glycinium) bis(hexafluorosilicate) glycine trisolvate [12]. Glycine hydrogen fluoride has been structurally and spectroscopically characterized. It crystallizes in an orthorhombic centrosymmetric structure (space group Pbca) and comprises three glycinium cations, three fluoride anions and also symmetric hydrogen diglycine cation and hydrogen bifluoride anion. Furthermore, we have made an interesting observation that this species, when ground to powder and left alone for a couple of weeks, turns at least partially into c-glycine. This fact is more important that it seems, because recently many papers have reported SHG activity in centrosymmetrical glycine compounds (see [8] and Refs. therein), an effect physically impossible. We think that in these cases a likewise transition had occurred, yielding non-centrosymmetrical c-glycine, responsible for the reported SHG signals. Moreover, later we noted that the surface of large transparent crystals of GlyHF in usual laboratory condition in time become nontransparent. The IR spectrum of scraped nontransparent layer showed that it represents c-glycine. 5. Supplementary material Supplementary crystallographic data for this paper have been deposited. These data can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retrieving.html (or from the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 36033), quoting this paper and the CCDC Number 779604. Acknowledgment This work was made possible by the research Grant PS1839 from the Armenian National Science and Education Fund (ANSEF) based in New York, USA. References [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12]
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