Vibrational, structural and theoretical studies of potassium dl -phenylglycinate

Journal of Molecular Structure 919 (2009) 303–311

Contents lists available at ScienceDirect

Journal of Molecular Structure journal homepage: www.elsevier.com/locate/molstruc

Vibrational, structural and theoretical studies of potassium

DL-phenylglycinate

Maria M. Ilczyszyn *, Tadeusz Lis, Maria Wierzejewska, Małgorzata Zatajska Faculty of Chemistry, Wrocław University, F.Joliot-Curie 14, 50-383 Wrocław, Poland

a r t i c l e

i n f o

Article history: Received 17 July 2008 Received in revised form 19 September 2008 Accepted 20 September 2008 Available online 7 October 2008 Keywords: Molecular structure Vibrational spectra DTF calculations Potassium DL-phenylglycinate

a b s t r a c t Phenylglycine, the simplest aromatic amino acid is interesting because of its potential applications as medical agent involved in the alkali ions transport in the biological and medical systems. Rather scarce structural and spectroscopic data concerning this molecule encouraged us to study a crystal structure and vibrational properties of the potassium DL-phenylglycinate salt (PGLYK). The crystal structure of PGLYK has been determined by X-ray diffraction at 100 K as monoclinic, space group P21/c, with Z = 4. The crystal comprises phenylglycine anions (PGLYA) and potassium cations. Each K+ is surrounded by five oxygens and one nitrogen which form a distorted octahedron. The intramolecular N–H  O hydrogen bond of 2.713(2) Å length is present in the studied crystal. The intermolecular N–H  p contacts have also been detected between adjacent amino groups and phenyl rings which may have an important contribution to the molecular packing observed for PGLYK. The infrared and Raman spectra of the crystalline sample are presented and discussed in relation to the theoretical predictions performed for the phenylglycine anion and potassium phenylglycinate at the B3LYP/6-311++G(2d,2p) level. The detailed interpretation of the vibrational spectra has been made on the basis of the calculated potential energy distribution matrix (PED). Ó 2008 Elsevier B.V. All rights reserved.

1. Introduction Apart from phenylalanine, tryptophan and tyrosine, phenylglycine (PGLY) belongs to the aromatic amino acids but, unlike those three, PGLY is a nonprotein amino acid. It appeared to be a very important starting material in production of the b-lactam drugs, e.g., semisynthetic penicillins and cephalosporins where it makes side chain as for example in Ampicillin, Cephalexin or Cephalor. Recently, genotoxic activity of PGLY and its halogenated derivatives has been reported [1,2]. L-Phenylglycine has a pharmacologic and analgesic efficacy profile similar to that of Pregabalin and Gabapentin [2]. Two latter are drugs widely used to relieve mostly neuropathic pain. Aromatic amino acids carry aromatic side chains. The presence of such structural group results in the unique properties of the particular amino acids and specific interaction between them and with other compounds. The aromatic amino acids exhibit hydrophobic properties which are very important for many biological processes in living cell. Phenylalanine, the simplest protein aromatic amino acid, is highly hydrophobic. Phenylglycine, very similar in structure to phenylalanine, also has such properties. Non-bonded interactions between aromatic rings are seen in many areas of chemistry and seem to make contribution to numerous chemical processes [3]. Such interactions are also very impor* Corresponding author. Tel.: +48 71 3757305; fax: +48 71 328 2348. E-mail address: [email protected] (M.M. Ilczyszyn). 0022-2860/$ - see front matter Ó 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2008.09.023

tant in medicine and biology. The vast majority of medicinal agents contain aromatic substituents and their differential recognition by proteins is likely dominated by aromatic–aromatic interactions [4]. As it was observed in the X-ray studies, the aromatic-aromatic interactions are crucially involved in the protein-deoxynucleic acid complexes [5]. Recently, cation–p (aromatic) interactions have been considered to be present in biological systems. It is supposed that the Na+ and K+ cations bound to the exposed p faces of aromatic acids associated with the ionic channels are responsible for the selective transport of the alkali metal ions through these channels into and out of the cells [6–8]. In spite of the interesting properties of PGLY, rather scarce structural and spectroscopic data concerning this molecule or its derivatives are available in the literature. Crystal structure of six PGLY salts with various inorganic acids [9–14] and spectroscopic studies of two of them [15,16] have been reported so far. In all these compounds PGLY appears as a cation and only one report on the vibrational spectrum of the phenylglycinate anion has been reported [17]. In this contribution the crystal structure and vibrational properties of the simple potassium DL-phenylglycinate salt (PGLYK) are presented and discussed. Interpretation of the experimental results is supported by the theoretical investigation of the geometry and vibrational frequencies of the isolated phenylglycinate anion (PGLYA) and potassium phenylglycinate salt (PGLYK) as model compounds. The aim of these calculations was threefold: a

304

M.M. Ilczyszyn et al. / Journal of Molecular Structure 919 (2009) 303–311

comparison between the experimental structural parameters determined from the X-ray analysis and theoretical geometry parameters, supporting the infrared and Raman spectra assignment by the comparison with the theoretical vibrational data and the attempt to reproduce the experimental spectra of the potassium phenylglycinate salt. 2. Experimental The PGLYK salt was obtained by mixing phenylglycine and KOH in a 1:2.5 ratio. The crystals suitable for X-ray studies were grown from saturated aqueous solution at room temperature in the dry nitrogen atmosphere. The X-ray studies were performed at 100 K by means of Kuma KM-4 CCD j-axis diffractometer with graphite-monochromatic Mo Ka radiation. The structure was solved by direct methods (program SHELXS97 [18]) and refined by the full-matrix least-squares method on all F2 data using the SHELXL97 [19] programs. Nonhydrogen atoms were refined with anisotropic thermal parameters; hydrogen atoms were included from Dq maps and were refined with isotropic thermal parameters. The room temperature infrared powder spectra were measured with the Bruker IFS-66 FT spectrometer as nujol and polychlorotrifluoroethylene mulls on KBr and CaF2 windows, respectively. The room temperature Raman powder spectrum was probed by means of the Nicolet IFS-860 instrument with the Raman attachment and Nd:YAG laser pumped by the diode laser (k = 1064 nm, power ca. 300 mW). The spectral resolution for both experiments was 2 cm1. All calculations were performed with the GAUSSIAN 03 [20] package of computer codes. Full geometry optimization was performed for the phenylglycine anion PGLYA and its potassium salt PGLYK at the B3LYP/6-311++(2d,2p) level. The harmonic vibrational frequencies were calculated following the structure optimization together with the infrared intensities and Raman scattering activities. Potential energy distributions (PED) of the normal modes were computed with the GAR2PED program [21] and the vibrational spectra were simulated using SYNSPEC program [22]. 3. Results and discussion 3.1. Crystal structure description The crystal data and structural refinement parameters are collected in Table 1. The selected bond distances and angles determined for the PGLYK crystal are gathered in Table 2. The geometrical parameters of the hydrogen bonds are also included. The geometry of the C6H5CHNH2COOK unit (PGLYK) is shown in Fig. 1 together with the atom numbering used throughout the paper. Both L and D enantiomers are present in the crystal characterized by the same set of the geometrical parameters. PGLYK crystallizes in the P21/c space group of the monoclinic system, Z = 4. The asymmetric part of the unit cell consists of the potassium cation and the phenylglycine anion (Fig. 1). The geometries around the potassium cation are depicted in Fig. 2. Each K+ is surrounded by six atoms: five oxygens and one nitrogen. The K–O/ N distances range from 2.648(2) to 2.911(2) Å showing a slightly distorted octahedral geometry around the K+ cation. The crystal packing is illustrated in Fig. 3. The crystal is built up from layers extending parallel to the (1 0 0) plane. The potassium cations and hydrophilic parts of the phenylglycine residues are situated inside the layer. The phenyl rings protrude from the layer and are arranged to each other in an off-center parallel orientation. Such orientation favors the

Table 1 Crystal data and structural refinement for potassium phenylglycinate. Empirical formula Formula weight Temperature Wavelength Crystal system Space group a (Å) b (Å) c (Å) b (°) Volume (Å3) Z Density (calculated) (g/cm3) Absorption coefficient (mm1) F(0 0 0) Crystal size (mm3) Theta range for the data collection (°) Index ranges Reflection collected Independent reflections Refinement method Data/parameters Goodness-of-fit F2 Final R indices [l > 2 sigma(I)]

C8H8KNO2 189.25 100(2) 0.71073 Å Monoclinic P21/c 14.472(6) 7.030(4) Å 8.721(4) Å 103.74(4)o 861.9(7) 4 1.459 0.572 392 0.50  0.18  0.13 3.24  37.43 23 6 h 6 24, 11 6 k 6 8, 14 6 l 6 14 12376 3974 Full-matrix least-squares on F2 3974/118 1.008 R1 = 0.0527, wR2 = 0.0801

p-stacking interactions which are expected to stabilize the PGLYK structure. The centroid–centroid separation between neighboring aromatic rings is less then 7.5 Å. According to McGaughey et al. [3] such distance proves a binding interaction between the rings. Two types of hydrogen bond interactions are presented in the crystal: the N–H  O and the N–H  p (Table 2). The former one is an intramolecular hydrogen bond of 2.713(2) Å length, the latter one is an interaction between the amino group and the phenyl ring with the N   p and H  p distances equal to 3.486 and 2.728 Å, respectively. The N–H   p interaction, just as the p-stacking interaction, may substantially contribute to the PGLYK structure stability. The phenylglycine moiety appears in PGLYK as an anion with non protonated amino group and deprotonated carboxylic group. The difference in the C–O distances (D(C–O) = (C1–O1)  (C1– O2)) is equal to 0.012 Å and is close to the corresponding value in the betaine molecular complexes with various acids [23]. The O2–C1–C2–N torsion angle, describing the mutual orientation of the amino and carboxylate groups equals 24.8(2)°. The C61–C11– C2–N dihedral angle indicating the relative orientation of the phenyl ring and the side-chain is equal to 135.4(1)°. The latter value is much higher than the corresponding torsion angle in other phenylglycine salts studied. This observation indicates that the phenylglycine moieties in PGLYK exhibit less folded conformation than in other phenylglycine compounds where the amino acid is present as a cation [9–12,14,24,25]. The phenyl rings of the phenylglycine residues in the studied crystal are slightly distorted from the planarity (see Table 2). The geometrical parameters of the glycine moieties: the C–C, C– N and COO bonds as well as the O–C–O, O–C–C and N–C–C angles are close to the corresponding parameters found in the a-glycine crystal [26]. 3.2. Geometry of PGA and PGK optimized at the B3LYP/6311++G(2d,2p) level Full geometry optimization of the phenylglycine anion (PGLYA) and the C6H5CHNH2COOK unit (PGLYK) was performed at the B3LYP/6-311++G(2d,2p) level. Both compounds may be considered as simplified models of the studied compound since they represent fragments of the studied crystal structure. In Table 2 the experimental geometry parameters are compared with those obtained from the B3LYP/6-311++G(2d,2p) method. As follows from this

305

M.M. Ilczyszyn et al. / Journal of Molecular Structure 919 (2009) 303–311

Table 2 Selected bond lengths (Å) and angles (°) determined by X-ray method for the potassium phenylglycinate crystal and calculated for the phenylglycinate anion (PGLYA) and the C6H5CHNH2COOK (PGLYK) at B3LYP/6-311++G(2d,2p) level. Parameter

Value Experimental

Parameters

Value

Calculated

Experimental

PGLYA

PGLYK

Calculated PGLYA

PGLYK

Bond lengths C(1)–O(1) C(1)–O(2) C(1)–C(2) C(2)–N C(2)–C(11) C(11)–C(21) C(21)–C(31) C(31)–C(41) C(41)–C(51) C(51)–C(61) C(61)–C(11) N–H(1N) N–H(2N)

1.2625(13) 1.2507(13) 1.5488(15) 1.4649(15) 1.5267(15) 1.3937(15) 1.3918(16) 1.3899(18) 1.3931(18) 1.3938(16) 1.3976(16) 0.90(2) 0.88(2)

1.244 1.251 1.602 1.466 1.511 1.400 1.391 1.392 1.393 1.390 1.400 1.012 1.020

1.260 1.265 1.548 1.461 1.527 1.397 1.391 1.392 1.391 1.391 1.396 1.014 1.014

Bond angles O(1)–C(1)–O(2) O(1)–C(1)–C(2) O(2)–C(1)–C(2) C(1)–C(2)–N N–C(2)–C(11) C(2)–C(11)–C(61) C(2)–C(11)–C(21) C(11)–C(21)–C(31) C(21)–C(31)–C(41) C(31)–C(41)–C(51) C(41)–C(51)–C(61) C(51)–C(61)–C(11) C(61)–C(11)–C(21)

126.09(9) 115.98(8) 117.87(8) 109.52(8) 115.15(8) 120.53(9) 120.83(10) 121.00(11) 120.12(10) 119.36(10) 120.44(11) 120.41(10) 118.65(9)

130.5 114.7 114.8 109.5 115.2 120.4 121.9 121.3 120.4 119.0 120.4 121.4 117.6

125.0 117.4 117.6 109.4 115.8 120.2 121.4 120.8 120.3 119.4 120.1 121.0 118.4

Torsion angles O(2)–C(1)–C(2)–N O(1)–C(1)–C(2)–N O(2)–C(1)–C(2)–C(11) O(1)–C(1)–C(2)–C(11) N–C(2)–C(11)–C(61) C(1)–C(2)–C(11)–C(61) N–C(2)–C(11)–C(21) C(1)–C(2)–C(11)–C(21)

24.84(12) 152.79(08) 95.98(10) 81.39(10) 135.44(10) 102.16(10) 45.10(13) 77.30(11)

23.8 156.7 102.7 76.8 144.3 92.5 37.8 85.3

31.2 150.4 95.9 82.6 -139.5 97.3 41.5 81.7

Torsion angles C(61)–C(11)–C(21)–C(31) C(2)–C(11)–C(21)–C(31) C(11)–C(21)–C(31)–C(41) C(21)–C(31)–C(41)–C(51) C(31)–C(41)–C(51)–C(61) C(21)–C(11)–C(61)–C(51) C(2)–C(11)–C(61)–C(51) C(41)–C(51)–C(61)–C(11)

0.70(15) 179.83(9) 0.56(16) 1.00(17) 0.18(17) 1.52(15) 179.01(9) 1.09(17)

0.5 178.5 0.9 0.4 0.4 0.5 178.5 0.1

0.1 179.1 0.0 0.1 0.1 0.2 179.2 0.1

X–K distances (X = O, N)a O(2)–Kiv O(1)–Kv O(1)–K

2.6514(15) 2.7570(16) 2.7807(13)

2.520

X–K distances (X = O, N)a O(2)–K O(1)–Kiii N–Ki

2.9109(13) 2.6478(15) 2.8919(17)

2.512

Hydrogen bond parameters

N. . .Y (Y = O, X1A)

N–H

H. . .Y (Y = O, X1A)

N–H. . .Y (Y = O, X1A)

N–H(2N) . . .O(2) N–H(1N) . . .X1Ab

2.7129(16) 3.486

0.88(2) 0.90(2)

2.33(2) 2.728

106.3(11)

a Symmetry codes: (i) x + 1, y + 1, z + 1; (ii) x + 1, y + 1, z + 2; (iii) x + 1, y  1/2, z + 3/2; (iv) x + 1, y + 1/2, z + 3/2; (v) x, y + 1/2, z  1/2; (vi) x, y + 1/2, z + 1/2. b Center of phenyl ring.

experiment. The deviations usually do not exceed 0.005 Å for bond lengths and 1° for bond angles. Slightly more pronounced differences have been noticed for the C–CO2 fragment and the values calculated for PGLYK seem to reproduce better the X-ray data than the corresponding values obtained for PGLYA. Larger discrepancies between experimental and calculated values, even in some cases up to 10°, are observed for dihedral angles showing rather high flexibility of the phenylglycine moiety and indicating strong influence of the crystal lattice on the skeleton of the molecule. The intramolecular N–H. . .O hydrogen bond reported in the Xray structure (2.713(2) Å) is also very well predicted by the present calculations with the N–H. . .O distance of 2.679 and 2.714 Å in PGLYA and PGLYK, respectively. The performed calculations for PGLYK were not fully successful to reproduce the K–O distances. The theoretical values of O(1)–K and O(2)–K distances are predicted to be almost equal (2.520 and 2.512 Å, respectively) while those obtained from the X-ray diffraction studies are apparently different and longer (2.781 and 2.911 Å). The predicted O(1)KO(2) angle of 52.8° is slightly overestimated as compared with the experimental value (46.3°). 3.3. Vibrational spectra and theoretical assignment Fig. 1. The structure unit of potassium phenylglycinate and the adopted atom numbering scheme.

comparison the bond lengths and angles calculated for the phenylglycine unit show, in most cases, a good agreement with the X-ray

Table 3 gathers the wavenumbers of the bands observed in the infrared and Raman spectra of the PGLYK polycrystalline sample. The theoretical band positions, infrared intensities (IIR), Raman scattering activities (SR) and Raman intensities (IR), derived from the SR values according to the procedure described in [27,28], for

306

M.M. Ilczyszyn et al. / Journal of Molecular Structure 919 (2009) 303–311

Fig. 2. The geometry around the K+ cation in the potassium phenylglycinate salt.

the PGLYA anion and PGLYK unit are also listed. In the last column of Table 3 the vibrational assignment is given, based on both the calculated potential energy distribution matrix (PED) and the literature data on benzene derivatives [29,30]. Figs. 4 and 5 compare the experimental FTIR and FTR of the potassium DL-phenylglycinate salt with the corresponding theoretical spectra calculated for PGLYA and PGLYK. The theoretical spectra were simulated using Lorentzian functions centered at the calculated scaled frequencies with the bandwidth-at-half-height equal to 9 or 7 cm1 for IR and R, respectively. The calculated frequencies were scaled by 0.964 above 2000 cm1 and by 0.985 for the 2000–500 cm1 spectral region for PGLYA and by 0.956 and 0.981 for PGLYK, respectively. The scaling factors were determined by the linear fitting with intercept zero. As it can be seen from Fig. 4 the theoretical spectrum obtained for the PGLYA anion reproduces relatively well the experimental infrared spectrum whereas that predicted for the PGLYK does not. When inspecting Fig. 5 the opposite conclusion may be drawn for the Raman spectra however the neither PGLYA nor PGLYK theoretical R spectrum gives a satisfactory agreement with the experimental results. One of the reason for this is probably the underestimation of the predicted intensity for the most intense Raman band situated at 999 cm1. 3.3.1. Vibrations of the phenyl ring Six C–H stretching modes (m2, m7a, m7b, m13, m20a, m20b) should be expected in the 3120–3010 cm1 region of the monosubstituted benzene derivatives [30]. Taking into account the selection rules, all of them are allowed in the infrared and Raman spectra. However, it happens quite often that in IR only three bands due to m20b, m20a and m2 can be separated from each other while in the Raman spectra only the m2 vibration is observable [30]. As it is seen from Table 3, it is not the case in the studied crystal since the phenylglycine anion gives rise to seven weak infrared absorptions due to the aromatic C–H stretching modes and five bands of medium

to strong intensity arising from these vibrations are present in the Raman spectrum. The above picture is in general agreement with the theoretical calculations where five modes with the most intense m2 band in the Raman spectrum are predicted. There are six normal modes of benzene derived from the C–C stretchings: m8a, m8b, m14, m19a, m19b and m1 vibrations. For the monosubstituted benzene the bands due to m8, m19, m14 are expected in the 1620–1570, 1515–1440 and 1350–1300 cm1 regions, respectively [30]. In the present study the m8a and m8b vibrations give rise to an intense infrared shoulder at 1615 cm1 and medium intense infrared band at 1581 cm1. The corresponding Raman bands are found at 1606 and 1582 cm1. The m19 mode usually has a significant in-plane C–H bending contribution and in monosubstituted benzenes splits into two m19a and m19b components [30]. In the present study two bands of medium intensity are observed at 1495 and 1452 cm1 in the infrared spectrum while only one weak Raman counterpart was found at 1453 cm1. According to the theoretical predictions the band observed at 1495 cm1 is due to the m19a mode coupled with the m18 (dCH) while lower wavenumber bands originate from the coupled m14 and m19b modes. The m14 vibration was identified at apparently lower wavenumbers (1301 (IR) and 1282 (R) cm1) for the crystalline phenylglycinium perchlorate sample [15]. The latter compound, in contrast with PGLYK, contains the phenylglycinium cations. There are five CH in-plane bending vibrations (m3, m9a, m15, m18a, m18b,) expected for the monosubstituted benzenes in the following regions [30]: 1330–1250 cm1 (m3), 1180–1170 cm1 (m9a), 1160– 1150 cm1 (m15), 1082–1065 cm1 (m18b) and 1030–1025 cm1 (m18a). The band due to the m3 mode exhibits very low intensity in both infrared and Raman spectra and its frequency is the least stable among the CH in-plane bending vibrations of monosubstituted benzenes. In agreement with the latter observation the m3 mode was not found in the studied spectra. Both m18a and m18b vibrations are, according to the calculated PED matrix, identified as components of weak bands at 1030, 1065 and 1098 cm1 coupled to other ring or substituent modes. Similar coupling was reported for the phenylglycine perchlorate case [15]. Two remaining in-plane CH deformation modes are observed at 1177 cm1 (IR, R) (m9a) and at 1160 cm1 (IR, R) (m15). The m1 normal mode of benzene has A1g symmetry: it is Raman active and is identified as second the most strong line in the Raman spectrum near 980 cm1 [30]. This mode is usually referred to as a substantially sensitive vibration. It couples with all sorts of the C–X (X denotes the benzene substituent) stretching and its position is strongly influenced by the total mass of polyatomic substituents [30]. The m12 mode of the B1u symmetry appears for benzene between 990 and 1010 cm1 and exhibits high Raman intensity and low infrared absorption. In monosubstituted benzenes both m1 and m12 vibrations belong to the same symmetry and are situated at similar wavenumbers. Thus, they might interact and mix to give intense Raman band near 1000 cm1 [15,30]. In the present investigation, the m1 and m12 modes are identified as two very intense bands at 1031 and 999 cm1 in the Raman spectrum. The performed calculations show, as expected, the strong coupling of the m1 and m12 modes (see Table S2). The in-plane ring deformation/skeletal CC vibrations, m6a and m6b give rise to the bands in the regions of 710–650 and 630–605 cm1, respectively for monosubstituted benzenes. In the present investigation two bands are observed in the corresponding regions at 687 (IR, R) and 618 cm1 (IR, R). According to the PED matrix the first one is assigned to the uncoupled m6a mode while the second one originates from m6b coupled to the d(CarCN) skeletal mode. Three normal modes due to the out-of-plane skeletal vibrations, m4, m16a and m16b, are expected in the vibrational spectra of monosubstituted benzenes [30]. The first one appears in a very narrow interval, between 680 and 700 cm1, as a very strong band in infrared and a very weak one in Raman. The m16a vibration is usually

M.M. Ilczyszyn et al. / Journal of Molecular Structure 919 (2009) 303–311

307

a

b

Fig. 3. The crystal packing in PGLYK. Projections: (a) along b axis; (b) along c axis.

found in the vicinity of 400 cm1 as a very weak band both in infrared and Raman. The third mode m16b localized in the 560–430 cm1 region is usually strongly coupled to the C–X skeletal vibrations. For the compound under study, the calculated PED matrix shows that the m4 mode is one of the components of the infrared intense band situated at 731 cm1. The m16b vibration gives rise to the weak band at 505 cm1 and, in agreement with the theoretical predictions, is strongly coupled to the out of plane skeletal c(CCC)arC mode. In turn, a weak band at 411 cm1 found in the Raman spectrum is attributed to the m16a mode. In monosubstituted benzenes several CH out-of-plane modes (m5, m10a, m10b, m11, m17a and m17b) are expected in the following re-

gions: 1000–970, 850–810, 910–880, 760–720 and 980–940 cm1 [30]. For the PGLYK sample four bands due to these vibrations are localized at 1010 (R), 723 (IR), 986 (IR, R) and 930 cm1 (IR, R) attributed, respectively to the m5, m11, m17a and m17b. The performed calculations predict that the m11 mode gives an important contribution to the strong infrared absorption at 731 cm1. 3.3.2. Vibrations of the amino acid chain 3.3.2.1. Vibrations of the –NH2 group. The bands due to the masNH2 and msNH2 vibrations are observed at 3378 and 3302 cm1, respectively both in infrared and Raman spectra. As expected, the masNH2 band exhibits higher intensity in infrared while the band assigned

308

M.M. Ilczyszyn et al. / Journal of Molecular Structure 919 (2009) 303–311

Table 3 in the vibrational spectra of crystalline NH2CHC6H5COOK and theoretical harmonic frequencies (m, Comparison of the experimental wavenumbers (cm1) of the bands observed 0 Å4/amu) and Raman intensities (IR) of PGLYA and PGLYK calculated at B3LYP/6-311++G(2d,2p). cm1), infrared intensities (IIR, km/mol), Raman scattering activities (SR, A Experimental spectra IR m vw vw w w w w w w

2990 2954 2931 2850 1615 1608 1581 1557 1540 1517 1495 1483 1452 1402 1395 1392 1355 1327 1254 1197 1177 1161 1155 1098 1065 1030

vw vw vw vw vssh vs m msh s msh m w m s ssh w s m w w vwsh w wsh vw w vw

vw vw vw w s

892 w 838 770 731 723 707 697 687 618 606 505 480

s vwsh s msh w s m vw m w vw

Assignmentb

Calculated spectra for PGLYK

m

IIR

SR

IR

m

IIR

SR

IR

3378 (0.23) 3302 (0.68)

3543 3420

4 67

74 54

25 20

3584 3499

11 16

36 94

12 33

maNH2 msNH2

3064 (1.4)

3179 3168

30 52

8 110

4 52

3183 3176

28 18

9 60

4 28

m20b(mCH) m13(mCH) + m20a(mCH)

3182 3150 3140

7 30 1

288 133 56

135 64 27

3190 3166 3159

14 4 2

336 120 29

156 57 14

m2(mCH) m7b(mCH) m7a(mCH)

3039

37

69

37

3059

19

60

32

mCH

1606 (0.52) sh 1596 (3.3) 1582 (1.29)

1631 1695 1609

35 343 39

98 14 10

219 29 23

1637 1582 1620

10 424 1

45 4 9

101 9 20

m8a(mCC) maCOO + dNH2 m8b(mCC)

1543 (0.29)

1616

145

20

45

1645

16

1

3

dNH2

1523

14

0

0

1528

10

1

1

m19a(mCC)

1482 1383

5 9

1 1

3 3

1488 1380

8 99

1 7

2 22

m19b(mCC) + m14(mCC) dCH + m3(dCH)

1349 1331 1301 1288 1216 1197 1173 1157 1127 1078 1047 982 1016 974

6 188 38 92 14 0 1 69 3 10 5 1 5 0

2 10 31 93 33 8 6 61 6 3 15 1 79 0

6 32 102 313 122 30 23 243 25 13 70 5 384 0

1353 1407 1338 1288 1217 1203 1181 1174 1126 1088 1049 1002 1020 988

26 187 9 2 14 0 2 12 4 8 4 0 0 0

4 23 9 4 17 4 6 16 3 2 13 1 49 1

13 66 28 14 63 13 21 64 12 8 59 1 237 1

m3(dCH) msCOO + qtNH2 dopCH + qtNH2 qtNH2 + dCH m(CarC) + dCH + m(CN) m9a(dCH) m15(dCH) dopCH + m(CC) m (CN) + m18b(dCH) m18b(dCH) + m(CN) m1(m CC) + m12(dCC) + m18a(dCH) m5(dCH) m12(dCC) + m1(mCC) m17a(dCH)

914 944 842 823

46 141 5 136

1 20 1 55

6 108 6 362

943 908 854 898

13 98 1 19

8 6 1 22

43 35 4 131

m17b (dCH) xNH2 + m(CN) m10(dCH) m(C–CO2) + d(CO2) + m(CCar)

849 779 729 704

43 6 9 38

5 10 7 1

31 71 54 8

842 789 741 711

116 8 29 28

1 7 2 1

4 48 17 1

xCO2 + xNH2 + d(C–C–C) d(CO2) + m11(dCH) m11 (dCH) + sCO2 + m4 (dCC) m11 (dCH)

674 634 609

17 0 16

1 3 4

9 28 39

702 635 619

50 0 28

1 4 2

3 34 16

d(CCN) + d(CO2) m6a(dCC) d(CarCN)) + m6b(dCC)

514 465 417 374 343 323

7 0 1 2 53 1

3 7 0 2 0 0

36 96 0 35 0 0

2 4

0 2

0 65

94 63 23

8 1 1

6 2 4

478 239 1338

6 6 0 1 52 14 12 14 24 14 11 1 15 1

1 2 1 1 1 1 1 2 1 1 3 2 3 5

3 27 1 17 6 21 30 83 6 8 191 190 709 2543

m16b(dCC) + c(CCC)arC m(CC) + d(CC = O) m16a(dCC) q(CO2) + q(NH2) qr(NH2)

239 220

513 485 415 385 304 260 335 201 218 151 103 61 29 16

Raman

3378 3302 3098 3080 3063 3055 3050 3038 3025

984 973 964 930 911

Calculated spectra for PGLYA a

3049 3038 3026 3001 2998 2953

(3.28) (1.01) (0.51) (0.28) (0.15) (0.46)

1453 (0.23) 1401 (0.44)

1354 1327 1253 1197 1178 1159

(0.42) (0.5) (0.4) (1.71) (1.4) (1.38)

1099 (0.33) 1067 (0.42) 1031 (2.11) 1010 (0.6) sh 999 (10) 986 (0.7)sh

928 (0.72) 908 (0.5) 891 850 843 779 732

(1.3) (0.3) (0.3) (1.75) (0.85)

687 618 608 505 480 411 364 307 253

(0.3) (1.95) (0.65) (0.34) (1.23) (0.38) (0.89) (0.36) (0.68)

230 175 149 129

(0.58) (0.63) (0.32) (0.28)

Abbreviations: m, stretching; d, bending; x, wagging; qr, rocking; qt, twisting. a The absolute Raman intensities are given in parentheses. b Denotation of the phenyl internal vibrations is taken from: [29,30].

Skeletal vibrations

309

M.M. Ilczyszyn et al. / Journal of Molecular Structure 919 (2009) 303–311

Experimental IR spectrum

Absorbance

0.75

0.50

0.25

0.00 4000

3500

3000

2500

2000

Wavenumber cm

1500

1000

500

1500

1000

500

1500

1000

500

-1

0.07

Relative Absorbance

0.06 0.05 0.04 0.03 0.02 0.01 0.00 4000

3500

3000

2500

2000

Wavenumber cm

-1

0.08 0.07

Relative abundance

0.06 0.05 0.04 0.03 0.02 0.01 0.00 4000

3500

3000

2500

2000

Wavenumber cm

-1

Fig. 4. The comparison of the experimental IR spectrum of the crystalline PGLYK and the theoretical IR spectra obtained for PGLYA (middle) and PGLYK (bottom). The theoretical spectra were simulated using Lorentzian functions centered at the calculated frequencies scaled by a factor of 0.964/0.956 (PGLYA/PGLYK) for the 4000– 2000 cm1 region and by 0.985/0.981 (PGLYA/PGLYK) for the 2000–400 cm1 region and with the bandwidth-at-half height equal to 9 cm1.

to msNH2 is more intense in the Raman spectrum. Similar position of the corresponding bands has been reported in Raman study of

sodium phenylglycinate in aqueous solution [17]. The difference between masNH2 and msNH2 positions is equal to ca. 80 cm1 and

310

M.M. Ilczyszyn et al. / Journal of Molecular Structure 919 (2009) 303–311

10

Experimental Raman spectrum

Raman intensity

8

6

4

2

0 4000

3500

3000

2500

2000

Wavenumber cm

1500

1000

500

1500

1000

500

1500

1000

500

-1

0.10

Relative Raman intensity

0.08

0.06

0.04

0.02

0.00 4000

3500

3000

2500

2000

Wavenumber cm

-1

0.10

Relative Raman intensity

0.08

0.06

0.04

0.02

0.00 4000

3500

3000

2500

2000

Wavenumber cm

-1

Fig. 5. The comparison of the experimental R spectrum of the crystalline PGLYK and the theoretical R spectra obtained for the PGLYA (middle) and PGLYK (bottom). The theoretical spectra were simulated using Lorentzian functions centered at the calculated frequencies scaled by a factor of 0.964/0.956 (PGLYA/PGLYK) for the 4000– 2000 cm1 region and by 0.985/0.981 (PGLYA/PGLYK) for the 2000–200 cm1 region and with the bandwidth-at-half height equal to 7 cm1.

it is close to the corresponding value observed for the non bonded NH2 group [29]. This observation confirms that the NH2 group is in-

volved in weak intramolecular hydrogen bond which does not affect its modes strongly. The corresponding scissoring mode dNH2

M.M. Ilczyszyn et al. / Journal of Molecular Structure 919 (2009) 303–311

311

is observed at ca. 1540 cm1 appearing as an intense infrared absorption and a weak Raman band. The torsional qtNH2 is localized at 1254 cm1 in both IR and R spectra. The latter mode, according to the calculations, also contributes to the msCOO and dopCH bands. In turn the wagging qwNH2 is found at 911 cm1 and contributes to the strong infrared band at 838 cm1 originating from the qwCO2 mode.

Additional data concerning the theoretical calculations are available as the Supporting Information.

3.3.2.2. Vibrations of the –CH fragment. Four bands due to the CH fragment are found in the studied spectra. The CH stretching mode is localized at ca. 2954 cm1 and three deformations, strongly coupled to other modes, are observed at 1402, 1327 and 1155 cm1.

Appendix A. Supplementary data

3.3.2.3. Vibrations of the –COO group. As follows from X-ray data, the carboxylic group of the glycine moiety in the studied crystal is ionized and characterized by similar C–O bond lengths of 1.262(2) and 1.251(2) Å. Accordingly, the bands due to the maCOO and msCOO modes should appear in the studied spectra in the 1650–1550 and 1400–1350 cm1 regions, respectively. The maCOO and msCOO vibrations in the studied crystal give rise to the intense absorptions at 1608 cm1 and 1355 cm1 in infrared while their Raman counterparts appear as strong and weak bands at 1596 cm1 and 1354 cm1, respectively. The unexpectedly high intensities of both stretching bands in Raman (maCOO) and in infrared (msCOO) is observed in the studied spectra. According to the theoretical predictions it must result from their significant coupling to the scissoring or twisting NH2 modes (see Table S2). 4. Summary The crystal structure of potassium DL-phenylglycinate has been determined and the adduct found to comprise phenylglycine anions and potassium cations. Each K+ is surrounded by one N and five O atoms which form slightly disordered octahedron. The intramolecular N–H  O hydrogen bond of 2.713(2) Å length between the NH2 group and one of the carboxylate oxygens is present in the studied crystal. In addition, two types of weak intermolecular interactions were detected: the N–H  p contacts of 3.486 Å between the amino group and the phenyl ring and the p-stacking interactions between the adjacent phenyl rings. The two latter interactions seem to be crucial for the molecular packing present in the PGLYK crystal. The results of geometry optimization at B3LYP/6311++G(2d,2p) level of the phenylglycine anion and potassium phenylglycinate show a good agreement with the experimental parameters obtained for the PGLYK unit. The infrared and Raman spectra of the crystalline potassium DLphenylglycinate are presented and discussed in relation to calculated vibrational spectra. The detailed interpretation of the IR and Raman spectra has been made on the basis of the potential energy distribution matrix (PED). 5. Supplementary data CCDC 656166 contains the supplementary crystallographic data for this paper. These data can be obtained free of charge via http:// www.ccdc.cam.ac.uk/deposit (or from the Cambridge Crystallographic Data Centre [email protected] Telephone: (44) 01223 762910 Fax: (44) 01223 336033, Postal Address: CCDC, 12 Union Road, Cambridge CB2 1EZ, UK.

Acknowledgement A grant of computer time from the Wrocław Center for Networking and Supercomputing is gratefully acknowledged.

Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.molstruc.2008.09.023. References [1] A. Boto, J.A. Gallardo, R. Hernández, F. Ledo, A. Muñoz, J.R. Murguía, M. Menacho-Márquez, A. Orjales, C.J. Saavedra, Bioorg. Med. Chem. Lett. 16 (2006) 6073. [2] J.L. Lynch, P. Honore, D.J. Anderson, W.H. Bunnelle, K.H. Mortell, Ch. Zhong, C.L. Wade, Ch.Z. Zhu, H. Xu, K.C. Marsh, Ch.-H. Lee, M.F. Jarvis, M. Gopalakrishnan, Pain 125 (2006) 136. [3] G.B. McGaughey, M. Gagné, A.K. Rappé, J. Biol. Chem. 273 (1998) 15458. [4] A.G. Gilman, T.W. Rall, A.S. Mies, P. Taylor, The Pharmaceutical basis of Therapeutics, eighth ed., MacGraw Hill Inc., New York, 1993. [5] T. Ishida, M. Doi, H. Ueda, M. Inoue, B.M. Scheldrick, J. Am. Chem. Soc. 110 (1988) 2286. [6] R.L. Nakamura, J.A. Angerson, R.F. Gabet, J. Biol. Chem. 272 (1997) 1011. [7] D.A. Dougherty, H.A. Lester, Angew. Chem. Int. Ed. 37 (1998) 2329. [8] R.C. Dunbar, J. Phys. Chem. A 104 (2000) 8067. [9] O. Angelova, R. Petrova, V. Radomieska, T. Kolev, Acta Cryst. C52 (1996) 2218. [10] S. Ravichandran, J.K. Dattagupta, Ch. Chakrabarti, Acta Cryst. C54 (1998) 499. [11] N. Srinivasan, B. Sridhar, R.K. Rajaram, Acta Cryst. E57 (2001) o754. [12] S. Ramaswamy, B. Shridhar, V. Ramakrishnan, R.K. Rajaram, Acta Cryst. E57 (2001) o1149. [13] K. Bouchouit, L. Bendheif, N. Benali-Cherif, Acta Cryst. E60 (2004) o272. [14] S. Bouacida, H. Merazig, P. Benard-Roucherulle, Acta Cryst. E62 (2006) o838. [15] S. Ramaswamy, R.K. Rajaram, V. Ramakrishnan, J. Raman Spectrosc. 33 (2002) 689. [16] T. Kolev, J. Mol. Struct. 846 (2007) 139. [17] J.L. Castro, M.R. López Ramírez, I. López Tocón, J.C. Otero, J. Mol. Struct. 651– 653 (2003) 601. [18] G.M. Sheldrick, SHELXS97. Program for Solution of Crystal Structures, University of Göttingen, Germany, 1997. [19] G.M. Sheldrick, SHELXL97. Program for Crystal Structure Refinement, University of Göttingen, Germany, 1997. [20] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery Jr., T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M. A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, and J.A. Pople, Gaussian 03, Revision D.01, Gaussian, Inc., Wallingford CT, 2004. [21] J.M.L. Martin, C. Van Alsenoy, GAR2PED, University of Antwerp, Antwerpen, Belgium, 1995. [22] K. Irikura, National Institute of Standards and Technology, Gaithesburg, MD 20899, USA, 1995. [23] D. Godzisz, M.M. Ilczyszyn, M. Ilczyszyn, J. Mol. Struct. 606 (2002) 123. [24] B.B. Ivanova, M.G. Arnaudov, Protein Pept. Lett. 13 (2006) 889. [25] B.B. Koleva, T. Kolev, S.Y. Zareva, M. Spiteller, J. Mol. Struct. 831 (2007) 165. [26] P.G. Jönsson, Å. Kvick, Acta Cryst. B28 (1972) 1827. [27] D. Michalska, R. Wysokin´ski, Chem. Phys. Lett. 403 (2005) 211. [28] R. Wysokin´ski, D. Michalska, D.C. Bien´ko, S. Ilakiamani, N. Sundaraganesan, K. Ramalingam, J. Mol. Struct. 791 (2006) 70. [29] B. Wojtkowiak, M. Chabanel, Spectrochimie moleculaire, Technique at Documentation, Paris, 1977. [30] G. Varsányi, Vibrational Spectra of Benzene Derivatives, Akadémiai Kiadó, Budapest, 1969.