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Crystal and molecular structure, hydrogen bonding and electrostatic interactions of bis(homarine) hydrogen perchlorate studied by X-ray diffraction, DFT calculations, FTIR and Raman spectroscopies
Journal of Molecular Structure 839 (2007) 99–106 www.elsevier.com/locate/molstruc
Crystal and molecular structure, hydrogen bonding and electrostatic interactions of bis(homarine) hydrogen perchlorate studied by X-ray diffraction, DFT calculations, FTIR and Raman spectroscopies M. Szafran *, A. Katrusiak, Z. Dega-Szafran Faculty of Chemistry, A. Mickiewicz University, 60780 Poznan´, Poland Received 21 September 2006; accepted 9 October 2006 Available online 21 December 2006
Abstract The crystals of bis(homarine)hydrogen perchlorate, (HOM)2HÆClO4, (1) are orthorhombic, space group C2/c, with a pair of HOM ˚ . In the homoconjugated cation, (HOMÆHÆHOM)+, the H-bondmolecules bridged by a symmetrical OÆHÆO hydrogen bond of 2.480(3) A ed proton is in centre of inversion. The COO groups are inclined by 29.98(18) to the plane of the pyridine rings, but pyridine rings are coplanar. The ClO4 anion additionally interacts electrostatically with the positively charged nitrogen atoms of the neighbouring HOM molecules. The most stable conformer of (HOM)2HÆClO4 (2) and four homoconjugated cations, (HOM)2H, (3–6) were analysed by the B3LYP/6-31G(d,p) calculations in order to determine the influence of the anion on the hydrogen bonds in the HOMÆHÆHOM unit. The FTIR spectrum of the (HOM)2HÆClO4 shows a broad and intense absorption in the 1500–400 cm1 region, typical of short hydrogen bonds. 2006 Elsevier B.V. All rights reserved. Keywords: Homarine; X-ray diffraction; B3LYP calculations; FTIR and Raman spectra; Hydrogen bond; Electrostatic interactions
1. Introduction Homarine, N-methyl-2-carboxy-pyridinium betaine, was isolated from animal tissues [1–3]. Synthetically homarine is prepared by methylation of picolinic acid with methyl iodide or methyl sulphate [4,5], and then treatment with silver oxide or barium hydroxide, respectively [3]. A better method is to pass aqueous solution of homarine methiodide through a quaternary ammonium resine (e.g. Dowex-1) in the hydroxide form. We have already reported on the crystal and molecular structures and vibrational spectra of homarinium chloride [6] and bis(homarine) hydrochloride monohydrate [7]. In this paper we describe the structure, hydrogen bond and *
Corresponding author. Tel.: +48 061 829 1320; fax: +48 061 865 8008. E-mail address: [email protected] (M. Szafran).
0022-2860/$ - see front matter 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2006.10.049
electrostatic interactions in bis(homarine) hydrogen perchlorate, (HOM)2HÆClO4. 2. Experimental 2.1. Synthesis Homarinium perchlorate, HOMHÆClO4, m.p. 137 C, and bis(homarine) hydrogen perchlorate, (HOM)2HÆClO4, m.p. 159–161 C, were prepared according to the method reported previously [7]. 2.2. Instrumentation X-ray diffraction measurements were carried out using a KUMA-4 CCD diffractometer. The structure of the compound was solved by direct methods with the
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SHELXS-97 program [8] and refined by the full-matrix least squares method on F2’s data using the SHELXL-97 [9] program. The crystal data and details concerning the data collection and structure refinement are given in Table 1, while the atomic coordinates in Table 2. The parameters
Table 1 Crystal data and structure refinement for bis(homarine) hydrogen perchlorate, (HOM)2HÆClO4 Empirical formula Formula weight Temperature Wavelength Crystal system Space group Unit cell dimensions
Volume Z Calculated density Absorption coefficient F(000) Crystal size h range for data collection Limiting indices h, k, l Reflections collected/unique/[R(int)] Completeness to h = 29.57 Data/restraints/parameters Goodness-of-fit on F2 Final R1/R2 indices [I > r(I)] R indices (all data) Largest diff. peak and hole
C14H15ClN2O8 374.73 293(2) K ˚ 0.71073 A Monoclinic C2/c ˚ a = 21.881(4) A ˚ b = 5.6980(11) A ˚ c = 12.991(2) A b = 94.72(3) ˚3 1618.6(6) A 4 1.538 g/cm3 0.284 mm1 776 0.3 · 0.2 · 0.1 mm 3.14–29.56 29/29, 7/6, 17/17 6363/2075/0.0672 91.6% 2075/0/123 1.156 R1 = 0.0507, wR2 = 0.1098 R1 = 0.0813, wR2 = 0.1259 ˚ 3 0.428 and 0.470 e A
in the CIF form are available as Electronic Supplementary Information from Cambridge Crystallographic Database Centre (CCDC 620204).
Table 2 Fractional atomic coordinates and equivalent isotropic displacement parameters of bis(homarine) hydrogen perchlorate Atoma
x
y
z
U(eq)
Cl(1) O(1P) O(2P) O(3P) N(1) C(2) C(3) C(4) C(5) C(6) C(7) C(8) O(1) O(2) H(3) H(4) H(5) H(6) H(71) H(72) H(73) H(1)
0 0.0585 0 0.0125(5) 0.1469(1) 0.1570(2) 0.1262(2) 0.0852(2) 0.0761(2) 0.1068(2) 0.1808(2) 0.1989(2) 0.2227(1) 0.2042(2) 0.1335 0.0640 0.0491 0.0998 0.2234 0.1763 0.1646 0.2500
0.3989(2) 0.4868(14) 0.1485(5) 0.4604(14) 0.8973(5) 0.7297(6) 0.7417(7) 0.9159(7) 1.0841(7) 1.0690(6) 0.9078(8) 0.5247(6) 0.4366(5) 0.4501(5) 0.6281 0.9206 1.2074 1.1811 0.8769 1.0606 0.7915 0.2500
0.2500 0.2623(6) 0.2500 0.3574(5) 0.1179(2) 0.0460(3) 0.0437(3) 0.0611(3) 0.0135(3) 0.1022(3) 0.2147(3) 0.0665(3) 0.0155(2) 0.1531(2) 0.0940 0.1217 0.0034 0.1533 0.2001 0.2453 0.2617 0
0.051(1) 0.151(3) 0.087(2) 0.174(3) 0.038(1) 0.035(1) 0.045(1) 0.052(1) 0.052(1) 0.046(1) 0.060(1) 0.044(1) 0.067(1) 0.068(1) 0.054 0.063 0.062 0.055 0.084 0.084 0.084 0.087
U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. a Coordinates of the second half of the bis(homarine) cation: x, y, 0.5 z.
Fig. 1. The molecular structure and atom labeling of bis(homarine) hydrogen perchlorate, (HOM)2HÆClO4. The hydrogen bond has been indicated by the dashed line and the thermal ellipsoids have been drawn at the 50% probability level. The H(1) atom is located at the center of inversion, and atoms Cl(1) and O(2P) of the perchlorate anion on a twofold axis parallel to [y].
M. Szafran et al. / Journal of Molecular Structure 839 (2007) 99–106
101
Fig. 2. Autostereogram of (HOM)2HÆClO4 structure viewed down [0 0 1]. The perchlorate anions are disordered (rotations about the Cl(1)–O(2P) bond parallel to [0 1 0]). The disordered overlapping perchlorate anions at lower z-coordinates, z c/2, have been drawn with double dashed lines representing Cl–O bonds, for clarity.
Table 3 ˚ ), angles and torsion angles (deg) for bis(homarine) hydrogen perchlorate determined by X-ray diffraction Bond lengths (A Bond lengths
Bond angles
N(1)–C(2) N(1)–C(6) N(1)–C(7) C(2)–C(3) C(2)–C(8) C(3)–C(4) C(4)–C(5) C(5)–C(6) C(8)–O(1) C(8)–O(2) Cl(1)–O(1P) Cl(1)–O(2P) Cl(1)–O(3P)
1.348(4) 1.334(4) 1.486(5) 1.369(5) 1.515(5) 1.363(5) 1.372(6) 1.359(5) 1.272(4) 1.212(4) 1.389(5) 1.427(4) 1.455(7)
C(2)–N(1)–C(6) C(2)–N(1)–C(7) C(6)–N(1)–C(7) N(1)–C(2)–C(3) N(1)–C(2)–C(8) C(2)–C(3)–C(4) C(3)–C(2)–C(8) C(3)–C(4)–C(5) C(4)–C(5)–C(6) N(1)–C(6)–C(5) O(1)–C(8)–O(2) O(1)–C(8)–C(2) O(2)–C(8)–C(2)
Torsion angles C(6)–N(1)–C(2)–C(3) C(6)–N(1)–C(2)–C(8) C(7)–N(1)–C(2)–C(3) C(7)–N(1)–C(2)–C(8) N(1)–C(2)–C(3)–C(4) C(2)–C(3)–C(4)–C(5) C(8)–C(2)–C(3)–C(4) C(3)–C(4)–C(5)–C(6)
1.1(5) 175.5(3) 176.1(3) 7.2(5) 1.1(5) 1.3(6) 175.6(4) 1.5(6)
C(2)–N(1)–C(6)–C(5) C(7)–N(1)–C(6)–C(5) C(4)–C(5)–C(6)–N(1) C(3)–C(2)–C(8)–O(1) N(1)–C(2)–C(8)–O(1) N(1)–C(2)–C(8)–O(2) C(3)–C(2)–C(8)–O(2) O(2)–C(8)–O(1)–H
120.4(3) 122.7(3) 116.9(3) 118.8(3) 120.6(3) 121.7(4) 120.6(3) 118.1(4) 119.4(4) 121.7(4) 126.2(4) 112.8(3) 120.8(4) 1.4(5) 176.0(3) 1.6(6) 29.2(5) 154.2(3) 30.6(5) 146.1(4) 4.4(5)
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Table 4 ˚ ngstroms, angles in degrees) for (HOM)2HClO4 and (HOM)2H Selected parameters (bond lengths in A (HOM)2HClO4
E (hartree)a l (debye) Erel (kcal/mol) O(1) O(1A) O(1)–H O(1A)–H O(1)HO(1A) C(8)–O(1) C(8A)–O(1A) C(8)–O(2) C(8A)–O(2A) O(1)–C(8)–O(2) O(1A)–C(8A)–O(2A) N(1)–C(2)–C(3)–C(4) N(1A)–C(2A)–C(3A)–C(4A) C(7)–N(1)–C(2)–C(8) C(7A)–N(1A)–C(2A)–C(8A) N(1)–C(2)–C(8)–O(1) N(1A)–C(2A)–C(8A)–O(1A) N(1)–C(2)–C(8)–O(2) N(1A)–C(2A)–C(8A)–O(2A) O(2)–C(8)–O(1)–H O(2A)–C(8A)–O(1A)–H N(1)–C(2)–N(1A)–C(2A) O(2)–O(1)–O(1A)–O(2A) MeN(1)–N(1A)Me N(1) ClO4 (x, y, z)b N(1A) ClO4 (x, y, z)b N(1) ClO4 (x, 1 y, z)b N(1A) ClO4 (x, 1 y, 0.5 + z)b N(1) ClO4 (x, 2 y, z)b N(1A) ClO4 (x, 2 y, 0.5 + z)b N(1) ClO4 (x, y 1, z)b N(1A) ClO4 (x, y 1, 0.5 z)b N(1) OH N(1A) O(A)H N(1) O@C N(1A) O(A)@C N(1) O(A)@C N(1A) O@C N(1) O(A)H N(1A) OH Average N O a b
(HOM)2H
X-ray
B3LYP
B3LYP
1 t-Linear
2 Bent
3 t-Linear
4 t-Linear
5 c-Linear
6 c-Linear
1713.669569 1.5717
952.755076 3.5107 0 2.401 1.202 1.208 170.4 1.286 1.186 1.227 1.227 129.7 129.7 2.2 2.2 0.06 0.05 42.8 42.7 137.6 137.7 23.0 22.9 177.0 82.0 141.8
952.753082 1.2437 1.671 2.411 1.206 1.206 177.3 1.285 1.285 1.226 1.226 129.4 129.4 0.8 0.8 2.9 2.9 162.9 163.0 18.4 18.4 5.2 5.2 103.6 84.0 131.2
952.753075 1.5344 1.256 2.411 1.205 1.207 177.0 1.285 1.284 1.226 1.226 129.4 129.5 0.9 0.8 3.1 2.9 161.9 160.9 19.7 20.5 3.9 4.6 60.7 75.2 85.7
952.753075 1.5354 1.256 2.411 1.205 1.207 177.0 1.285 1.284 1.225 1.226 129.4 129.5 0.9 0.8 3.1 2.9 161.9 160.9 19.7 20.5 3.9 4.6 60.7 75.2 85.7
2.883 2.883 3.491 3.491 4.321 4.327 4.937 4.937 3.909
3.578 3.578 2.879 2.879 6.095 6.094 5.700 5.700 4.563
3.575 3.572 2.878 2.880 5.757 5.992 5.681 5.699 4.504
3.575 3.572 2.878 2.880 5.757 5.992 5.851 5.699 4.527
2.480(3) 1.240(2) 1.240(2) 180 1.272(4) 1.272(4) 1.212(4) 1.212(4) 126.2(4) 126.2(4) 1.1(5) 1.1(5) 7.2(5) 7.2(5) 154.2(3) 154.2(3) 30.6(5) 30.6(5) 4.4(5) 4.4(5) 180 180 180 6.510 6.510 3.964 3.964 5.380 5.380 6.518 6.518 3.526 3.526 2.884 2.884
2.437 1.067 1.400 160.6 1.308 1.268 1.217 1.234 127.6 130.9 1.0 1.4 0.9 4.7 161.4 144.0 18.6 38.9 25.9 53.2 93.2 177.6 127.7 3.551 5.967
3.573 3.523 2.889 2.938 6.829 6.277 5.332 5.533 4.609
E(B3LYP/6-31G(d,p)) of ClO4 760.798430 hartree. Symmetry codes.
FTIR spectra were recorded on a Bruker IFS 113v spectrometer, which was evacuated to avoid water and CO2 absorptions, at a 2 cm1 resolution in Nujol and Fluorolube mulls. Raman spectrum was recorded on a Magna 760 Nicolet operating at the 1064 nm exciting line of a Nd:YAG laser. Each FTIR and Raman spectrum consists of 250 scans. The centre of gravity of the broad absorption in the 1500–400 cm1 region, m 0 = m log(Io/I) dm/log(Io/ I) dm, where Io is the intensity of radiation incident on the sample at wavenumber m and I is the transmitted intensity, calculated with dm = 0.96 cm1 is at 908 cm1.
2.3. B3LYP calculations The calculations were performed using the Gaussian 03 package [10] and the B3LYP [11–13] methods in conjunction with the basis set of 6-31G(d,p) [14]. 3. Results and discussion Picolinic acid on heating with an excess of CH3I is converted into the bis(homarine) hydroiodide (2:1 complex) [6]. In exactly the same conditions, nicotinic acid gave
M. Szafran et al. / Journal of Molecular Structure 839 (2007) 99–106
103
Fig. 3. Comparison of X-Ray (1) and B3LYP/6-31G(d,p) (2–6) structures.
trigonelline (TRG) hydroiodide (N-methyl-3-pyridiniumcarboxy iodide, 1:1 complex) [15,16]. Hydroiodides are converted into betaines. 3.1. Crystal structure The structure of (HOM)2HÆClO4 with the atom numbering is shown in Fig. 1 and the molecular packing in the crystal in Fig. 2. The bond lengths, bond angles, and torsion angles are listed in Tables 3 and 4. Two molecules of HOM are bridged by a proton to form a homoconjugated cationic system (HOMÆHÆHOM)+ with a short, symmetrical O H O hydrogen bond with the O O distance of ˚ . Because the hydrogen bonded HOM molecules 2.480(3) A are symmetrically equivalent, the (HOM)2H cation is similar to the Type A acid salts of carboxylic acids [17]. In (HOM)2HÆClÆH2O [7], (TRG)2HÆClÆH2O [18], (MIN)2 HÆClÆH2O [19], and bis(quinoline betaine) hydrogen perchlorate [20] H-bonded protons are located asymmetrically, similarly as in the pseudo-Type A acid salts of carboxylic acids. The (HOM)2H cations are arranged approximately parallel in the crystal lattice, as shown in Fig. 2. The carboxy groups participating in the hydrogen bond are planar. The angle between the planes through the rings and COO
groups is 29.98(18). The ClO4 anions are also located symmetrically relative to both positively charged nitrogen atom in HOMÆHÆHOM cations (see Nþ ClO4 distances in Table 4) and the hydrogen bond in the crystal is centrosymmetric. 3.2. B3LYP/6-31G(d,p) calculations Table 4 shows the abbreviations of the molecules investigated, their energies, dipole moments and selected geometrical parameters. In Fig. 3 the crystal linear structure (1) is compared with those optimized by the DFT calculations for isolated units (2–6). There are three important features contributing to the stability of the structures of the molecules in the crystal and the isolated ones (as present in the gas phase): (i) hydrogen bond distance, (ii) electrostatic interactions between the oppositely charged groups and atoms (between the positively charged nitrogen atom with anion and oxygen atoms of COO groups) and (iii) dipole moment. On going from crystal to isolate molecule the inter-molecular (isotropic) electrostatic (Coulombic) attractions disappear but intramolecular (anisotropic) ones become stronger. In consequence the optimized structure of (HOM)2HÆClO4 (2) is different (bent) in comparison with that in the crystal (linear) (1).
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In the optimized (HOM)2H cations (3–6) the hydrogen bonds are shorter in comparison with 1 and 2 (Table 4). In 3 and 4 the N–Me groups, similarly as in 1, are located on the opposite sides of OÆHÆO bridge (t-linear), while in 5 and 6 they are on the same side (c-linear). Their structures are stabilized by the electrostatic interactions between N+ and oxygen atoms. Their relative energies increase with increasing average N+ O distances (Table 4). 3.3. FTIR and Raman spectra In the FTIR spectra of HOMHÆClO4 the mC@O band is at 1744 cm1 (Fig. 4a) and indicates that a proton from the acid is transferred to HOM. The mOH absorption is located in the 3090 cm1 region. The FTIR spectrum of (HOM)2HÆClO4 is dominated by a broad and strong absorption in the range of 1500–400 cm1, typical ˚ . A similar broad of hydrogen bonds shorter than 2.5 A absorption appears in the 2:1 spectra of trigonelline [16], other betaines [21] and type A acid salts of carbox-
Absorbance
2,0
ylic acids [22,23]. This absorption is attributed to the (OHO) stretching and bending vibrations of a short hydrogen bond [24–26]. The continuous absorption and the skeletal vibrations overlap, but the latter feature can be distinguished in the second-derivative spectroscopy, d2 (Fig. 4c). In the second-derivative spectra, the minima have the same wavenumbers as the maxima in the absorption spectra [27], but their intensities vary inversely with the fourth power of the half-width of the absorption bands. The observed wavenumbers in (HOM)2HClO4 and their tentative absorption, based on comparison with the spectrum of HOMHÆCl, are listed in Table 5. In the Raman spectra of the 2:1 complexes the broad absorption is absent (Fig. 4b). The frequency plot of the negative bands in the d2 spectrum versus the Raman frequencies is linear with a unit slope (Fig. 5). Thus the derivative spectrometry can be used to estimate frequencies of the narrow bands covered by the broad absorption due to the stretching and bending OHO vibrations.
a
1,5 1,0 0,5 0,0
Ranam intensity
7,5
b
5,0
2,5
0,0
Arbitrary units
0,2
c
0,0 -0,2 -0,4
3500
3000
2500
2000
1500
1000
500
-1 Wavenumbers (cm ) Fig. 4. Vibrational spectra of (HOM)2HClO4: (a) FTIR (suspension in Nujol and Fluorolube); (b) Raman; (c) second-derivative spectrum; dotted line – FTIR spectrum of HOMHÆClO4.
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105
Table 5 Vibrational frequencies of homarine hydrochloride, HOMHÆCl (t), bis(homarine) hydrochloride monohydrate, (HOM)2HClÆH2O and bis(homarine) hydrogen perchlorate, (HOM)2HClO4 HOMHÆCla Raman
3098 3062
(HOM)2HClÆH2Ob FTIR
3092 3082sh 3064 3047sh
Raman
FTIR
3080
3366 3264 3142 3077
3045 3035 3010 2969
3044
2977
3010 2975
1721 1615
2650–2146 1789 1722 1615
1676 1627
1587
1586
1585
1748 1650 1628 1583
1515
1500
1517
1509
1451 1429 1389
1449 1431 1389
1456 1442 1405 1373
1458 1403 1354
1311 1290
1311 1288
1193 1168
1228 1191 1166
1296 1239
1289 1243
1109 1065 1053
1066 1050
913 898
921
813 786
919 898 817 813 772
762
762
762
717 631
723 682 666
686
569
466 449 422 a b
1137
3102 3067
2981
840 829 806
928 915 846 807 791 771
1724 1649 1628 1599 1582 1507 1488 1453 1439 1401 1356 1325 1310 1288
1191 1166 1150 1136
925 912 835 820 791
664
767 744 720 685 668
555
554
575 556
470 442
487 442
722
Approximate assignments FTIR
3143 3101 3088 3063
3142 3102 3086 3061
2981
2981
1742 1622
1741 1621
1582
1584
1583
1509
1509
1454 1431 1403 1376 1345
1455 1430 1402
1286
1286
1171 1165 1094 1085
1170 1145 1096 1081 1068 1052 1027 983 920
1450
1356
1173 1109
1053
932 914 898 839 786
772
733 717 683 631 617 565
695 668 623 560
485 442 429
466 450 422
442
H2O H2O mCH mCH mCH mCH mCH mCH mMe mOH
1686 1619
521
Data from Ref. [6]. Data from Ref. [7]; d2 – second-derivative frequencies.
d2
1500–400
1119 1034
1067 1050
569 534 461 434
3139 3077 3054 3043 3020 3004 2965
Raman
1500–400
1175 1168 1151 1118
1168
(HOM)2HClO4 d2
mCO mCC mCC mCC + mCN bMe + bCH bMe + bCH bMe bMe + bCH bOH bOH
1348
833 804 790 773 760
694 683 624 561 547 526 462 442
bOH mCO + bOH + mCC bCH + mCC + mCN bCH + mCC + mCN bCH + bCN + mCN bMe + bRing + mCO mClO4 + bMe bMe + bCH + bRing mCC + bMe
cCH cCH cCH mCN + bRing bCO + sCO + mCC cCH sCO + sRing sRing + sCC + sCO bRing + bCO
bRing + sRing + bCO bRing + bCO sRing + bCN sRing + cCN sRing
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References
3000
[1] [2] [3] [4] [5] [6]
2500
d
2
2000 1500
[7]
1000
[8]
500
[9]
500
1000 1500 2000 2500 -1 Raman wavenumbers/cm
3000
[10]
Fig. 5. Relation between d2 and Raman frequencies for (HOM)2HClO4; m(d2) = 4.262 + 1.002 m(Raman), r2 = 0.9998.
4. Conclusions According to the X-ray data, in the crystal of (HOM)2HÆClO4 a pair of homarine molecules are joined by a hydrogen bond involving the proton to form a homoconjugated cation, featuring the short and symmetrical hydrogen ˚ . The bond with the O O distance equal to 2.480(3) A homarine units are equivalent as a result of electrostatic interactions with the ClO4 anion. The ClO4 anions are located symmetrically relative to both positively charged nitrogen atoms in HOMÆHÆHOM cations The COO groups are inclined at 29.98(18) to the plane of the pyridine rings, which are coplanar. The hydrogen bond in (HOM)2HÆClO4 is similar to that in Type A acid salts of carboxylic acids and it can be described by a potential energy function with a single minimum. For the isolated molecule there is no intermolecular (isotropic) electrostatic (Coulombic) attractions characteristic of the crystal structure, but intramolecular (anisotropic) interactions become more important. In consequence, the optimized structure of (HOM)2HÆClO4 (2) is different (bent) than in the crystal (linear) (1). The optimised HOMÆHÆHOM cations, 3–6, are linear with shorter hydrogen bonds relative to that in 1. Their energy decreases with increasing average N+ O distances (Table 4).
Acknowledgement The calculations were performed at the Poznan´ Supercomputing and Networking Centre.
[11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23]
[24] [25] [26] [27]
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Crystal and molecular structure, hydrogen bonding and electrostatic interactions of bis(homarine) hydrogen perchlorate studied by X-ray diffraction, DFT calculations, FTIR and Raman spectroscopies M. Szafran *, A. Katrusiak, Z. Dega-Szafran Faculty of Chemistry, A. Mickiewicz University, 60780 Poznan´, Poland Received 21 September 2006; accepted 9 October 2006 Available online 21 December 2006
Abstract The crystals of bis(homarine)hydrogen perchlorate, (HOM)2HÆClO4, (1) are orthorhombic, space group C2/c, with a pair of HOM ˚ . In the homoconjugated cation, (HOMÆHÆHOM)+, the H-bondmolecules bridged by a symmetrical OÆHÆO hydrogen bond of 2.480(3) A ed proton is in centre of inversion. The COO groups are inclined by 29.98(18) to the plane of the pyridine rings, but pyridine rings are coplanar. The ClO4 anion additionally interacts electrostatically with the positively charged nitrogen atoms of the neighbouring HOM molecules. The most stable conformer of (HOM)2HÆClO4 (2) and four homoconjugated cations, (HOM)2H, (3–6) were analysed by the B3LYP/6-31G(d,p) calculations in order to determine the influence of the anion on the hydrogen bonds in the HOMÆHÆHOM unit. The FTIR spectrum of the (HOM)2HÆClO4 shows a broad and intense absorption in the 1500–400 cm1 region, typical of short hydrogen bonds. 2006 Elsevier B.V. All rights reserved. Keywords: Homarine; X-ray diffraction; B3LYP calculations; FTIR and Raman spectra; Hydrogen bond; Electrostatic interactions
1. Introduction Homarine, N-methyl-2-carboxy-pyridinium betaine, was isolated from animal tissues [1–3]. Synthetically homarine is prepared by methylation of picolinic acid with methyl iodide or methyl sulphate [4,5], and then treatment with silver oxide or barium hydroxide, respectively [3]. A better method is to pass aqueous solution of homarine methiodide through a quaternary ammonium resine (e.g. Dowex-1) in the hydroxide form. We have already reported on the crystal and molecular structures and vibrational spectra of homarinium chloride [6] and bis(homarine) hydrochloride monohydrate [7]. In this paper we describe the structure, hydrogen bond and *
Corresponding author. Tel.: +48 061 829 1320; fax: +48 061 865 8008. E-mail address: [email protected] (M. Szafran).
0022-2860/$ - see front matter 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2006.10.049
electrostatic interactions in bis(homarine) hydrogen perchlorate, (HOM)2HÆClO4. 2. Experimental 2.1. Synthesis Homarinium perchlorate, HOMHÆClO4, m.p. 137 C, and bis(homarine) hydrogen perchlorate, (HOM)2HÆClO4, m.p. 159–161 C, were prepared according to the method reported previously [7]. 2.2. Instrumentation X-ray diffraction measurements were carried out using a KUMA-4 CCD diffractometer. The structure of the compound was solved by direct methods with the
100
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SHELXS-97 program [8] and refined by the full-matrix least squares method on F2’s data using the SHELXL-97 [9] program. The crystal data and details concerning the data collection and structure refinement are given in Table 1, while the atomic coordinates in Table 2. The parameters
Table 1 Crystal data and structure refinement for bis(homarine) hydrogen perchlorate, (HOM)2HÆClO4 Empirical formula Formula weight Temperature Wavelength Crystal system Space group Unit cell dimensions
Volume Z Calculated density Absorption coefficient F(000) Crystal size h range for data collection Limiting indices h, k, l Reflections collected/unique/[R(int)] Completeness to h = 29.57 Data/restraints/parameters Goodness-of-fit on F2 Final R1/R2 indices [I > r(I)] R indices (all data) Largest diff. peak and hole
C14H15ClN2O8 374.73 293(2) K ˚ 0.71073 A Monoclinic C2/c ˚ a = 21.881(4) A ˚ b = 5.6980(11) A ˚ c = 12.991(2) A b = 94.72(3) ˚3 1618.6(6) A 4 1.538 g/cm3 0.284 mm1 776 0.3 · 0.2 · 0.1 mm 3.14–29.56 29/29, 7/6, 17/17 6363/2075/0.0672 91.6% 2075/0/123 1.156 R1 = 0.0507, wR2 = 0.1098 R1 = 0.0813, wR2 = 0.1259 ˚ 3 0.428 and 0.470 e A
in the CIF form are available as Electronic Supplementary Information from Cambridge Crystallographic Database Centre (CCDC 620204).
Table 2 Fractional atomic coordinates and equivalent isotropic displacement parameters of bis(homarine) hydrogen perchlorate Atoma
x
y
z
U(eq)
Cl(1) O(1P) O(2P) O(3P) N(1) C(2) C(3) C(4) C(5) C(6) C(7) C(8) O(1) O(2) H(3) H(4) H(5) H(6) H(71) H(72) H(73) H(1)
0 0.0585 0 0.0125(5) 0.1469(1) 0.1570(2) 0.1262(2) 0.0852(2) 0.0761(2) 0.1068(2) 0.1808(2) 0.1989(2) 0.2227(1) 0.2042(2) 0.1335 0.0640 0.0491 0.0998 0.2234 0.1763 0.1646 0.2500
0.3989(2) 0.4868(14) 0.1485(5) 0.4604(14) 0.8973(5) 0.7297(6) 0.7417(7) 0.9159(7) 1.0841(7) 1.0690(6) 0.9078(8) 0.5247(6) 0.4366(5) 0.4501(5) 0.6281 0.9206 1.2074 1.1811 0.8769 1.0606 0.7915 0.2500
0.2500 0.2623(6) 0.2500 0.3574(5) 0.1179(2) 0.0460(3) 0.0437(3) 0.0611(3) 0.0135(3) 0.1022(3) 0.2147(3) 0.0665(3) 0.0155(2) 0.1531(2) 0.0940 0.1217 0.0034 0.1533 0.2001 0.2453 0.2617 0
0.051(1) 0.151(3) 0.087(2) 0.174(3) 0.038(1) 0.035(1) 0.045(1) 0.052(1) 0.052(1) 0.046(1) 0.060(1) 0.044(1) 0.067(1) 0.068(1) 0.054 0.063 0.062 0.055 0.084 0.084 0.084 0.087
U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. a Coordinates of the second half of the bis(homarine) cation: x, y, 0.5 z.
Fig. 1. The molecular structure and atom labeling of bis(homarine) hydrogen perchlorate, (HOM)2HÆClO4. The hydrogen bond has been indicated by the dashed line and the thermal ellipsoids have been drawn at the 50% probability level. The H(1) atom is located at the center of inversion, and atoms Cl(1) and O(2P) of the perchlorate anion on a twofold axis parallel to [y].
M. Szafran et al. / Journal of Molecular Structure 839 (2007) 99–106
101
Fig. 2. Autostereogram of (HOM)2HÆClO4 structure viewed down [0 0 1]. The perchlorate anions are disordered (rotations about the Cl(1)–O(2P) bond parallel to [0 1 0]). The disordered overlapping perchlorate anions at lower z-coordinates, z c/2, have been drawn with double dashed lines representing Cl–O bonds, for clarity.
Table 3 ˚ ), angles and torsion angles (deg) for bis(homarine) hydrogen perchlorate determined by X-ray diffraction Bond lengths (A Bond lengths
Bond angles
N(1)–C(2) N(1)–C(6) N(1)–C(7) C(2)–C(3) C(2)–C(8) C(3)–C(4) C(4)–C(5) C(5)–C(6) C(8)–O(1) C(8)–O(2) Cl(1)–O(1P) Cl(1)–O(2P) Cl(1)–O(3P)
1.348(4) 1.334(4) 1.486(5) 1.369(5) 1.515(5) 1.363(5) 1.372(6) 1.359(5) 1.272(4) 1.212(4) 1.389(5) 1.427(4) 1.455(7)
C(2)–N(1)–C(6) C(2)–N(1)–C(7) C(6)–N(1)–C(7) N(1)–C(2)–C(3) N(1)–C(2)–C(8) C(2)–C(3)–C(4) C(3)–C(2)–C(8) C(3)–C(4)–C(5) C(4)–C(5)–C(6) N(1)–C(6)–C(5) O(1)–C(8)–O(2) O(1)–C(8)–C(2) O(2)–C(8)–C(2)
Torsion angles C(6)–N(1)–C(2)–C(3) C(6)–N(1)–C(2)–C(8) C(7)–N(1)–C(2)–C(3) C(7)–N(1)–C(2)–C(8) N(1)–C(2)–C(3)–C(4) C(2)–C(3)–C(4)–C(5) C(8)–C(2)–C(3)–C(4) C(3)–C(4)–C(5)–C(6)
1.1(5) 175.5(3) 176.1(3) 7.2(5) 1.1(5) 1.3(6) 175.6(4) 1.5(6)
C(2)–N(1)–C(6)–C(5) C(7)–N(1)–C(6)–C(5) C(4)–C(5)–C(6)–N(1) C(3)–C(2)–C(8)–O(1) N(1)–C(2)–C(8)–O(1) N(1)–C(2)–C(8)–O(2) C(3)–C(2)–C(8)–O(2) O(2)–C(8)–O(1)–H
120.4(3) 122.7(3) 116.9(3) 118.8(3) 120.6(3) 121.7(4) 120.6(3) 118.1(4) 119.4(4) 121.7(4) 126.2(4) 112.8(3) 120.8(4) 1.4(5) 176.0(3) 1.6(6) 29.2(5) 154.2(3) 30.6(5) 146.1(4) 4.4(5)
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Table 4 ˚ ngstroms, angles in degrees) for (HOM)2HClO4 and (HOM)2H Selected parameters (bond lengths in A (HOM)2HClO4
E (hartree)a l (debye) Erel (kcal/mol) O(1) O(1A) O(1)–H O(1A)–H O(1)HO(1A) C(8)–O(1) C(8A)–O(1A) C(8)–O(2) C(8A)–O(2A) O(1)–C(8)–O(2) O(1A)–C(8A)–O(2A) N(1)–C(2)–C(3)–C(4) N(1A)–C(2A)–C(3A)–C(4A) C(7)–N(1)–C(2)–C(8) C(7A)–N(1A)–C(2A)–C(8A) N(1)–C(2)–C(8)–O(1) N(1A)–C(2A)–C(8A)–O(1A) N(1)–C(2)–C(8)–O(2) N(1A)–C(2A)–C(8A)–O(2A) O(2)–C(8)–O(1)–H O(2A)–C(8A)–O(1A)–H N(1)–C(2)–N(1A)–C(2A) O(2)–O(1)–O(1A)–O(2A) MeN(1)–N(1A)Me N(1) ClO4 (x, y, z)b N(1A) ClO4 (x, y, z)b N(1) ClO4 (x, 1 y, z)b N(1A) ClO4 (x, 1 y, 0.5 + z)b N(1) ClO4 (x, 2 y, z)b N(1A) ClO4 (x, 2 y, 0.5 + z)b N(1) ClO4 (x, y 1, z)b N(1A) ClO4 (x, y 1, 0.5 z)b N(1) OH N(1A) O(A)H N(1) O@C N(1A) O(A)@C N(1) O(A)@C N(1A) O@C N(1) O(A)H N(1A) OH Average N O a b
(HOM)2H
X-ray
B3LYP
B3LYP
1 t-Linear
2 Bent
3 t-Linear
4 t-Linear
5 c-Linear
6 c-Linear
1713.669569 1.5717
952.755076 3.5107 0 2.401 1.202 1.208 170.4 1.286 1.186 1.227 1.227 129.7 129.7 2.2 2.2 0.06 0.05 42.8 42.7 137.6 137.7 23.0 22.9 177.0 82.0 141.8
952.753082 1.2437 1.671 2.411 1.206 1.206 177.3 1.285 1.285 1.226 1.226 129.4 129.4 0.8 0.8 2.9 2.9 162.9 163.0 18.4 18.4 5.2 5.2 103.6 84.0 131.2
952.753075 1.5344 1.256 2.411 1.205 1.207 177.0 1.285 1.284 1.226 1.226 129.4 129.5 0.9 0.8 3.1 2.9 161.9 160.9 19.7 20.5 3.9 4.6 60.7 75.2 85.7
952.753075 1.5354 1.256 2.411 1.205 1.207 177.0 1.285 1.284 1.225 1.226 129.4 129.5 0.9 0.8 3.1 2.9 161.9 160.9 19.7 20.5 3.9 4.6 60.7 75.2 85.7
2.883 2.883 3.491 3.491 4.321 4.327 4.937 4.937 3.909
3.578 3.578 2.879 2.879 6.095 6.094 5.700 5.700 4.563
3.575 3.572 2.878 2.880 5.757 5.992 5.681 5.699 4.504
3.575 3.572 2.878 2.880 5.757 5.992 5.851 5.699 4.527
2.480(3) 1.240(2) 1.240(2) 180 1.272(4) 1.272(4) 1.212(4) 1.212(4) 126.2(4) 126.2(4) 1.1(5) 1.1(5) 7.2(5) 7.2(5) 154.2(3) 154.2(3) 30.6(5) 30.6(5) 4.4(5) 4.4(5) 180 180 180 6.510 6.510 3.964 3.964 5.380 5.380 6.518 6.518 3.526 3.526 2.884 2.884
2.437 1.067 1.400 160.6 1.308 1.268 1.217 1.234 127.6 130.9 1.0 1.4 0.9 4.7 161.4 144.0 18.6 38.9 25.9 53.2 93.2 177.6 127.7 3.551 5.967
3.573 3.523 2.889 2.938 6.829 6.277 5.332 5.533 4.609
E(B3LYP/6-31G(d,p)) of ClO4 760.798430 hartree. Symmetry codes.
FTIR spectra were recorded on a Bruker IFS 113v spectrometer, which was evacuated to avoid water and CO2 absorptions, at a 2 cm1 resolution in Nujol and Fluorolube mulls. Raman spectrum was recorded on a Magna 760 Nicolet operating at the 1064 nm exciting line of a Nd:YAG laser. Each FTIR and Raman spectrum consists of 250 scans. The centre of gravity of the broad absorption in the 1500–400 cm1 region, m 0 = m log(Io/I) dm/log(Io/ I) dm, where Io is the intensity of radiation incident on the sample at wavenumber m and I is the transmitted intensity, calculated with dm = 0.96 cm1 is at 908 cm1.
2.3. B3LYP calculations The calculations were performed using the Gaussian 03 package [10] and the B3LYP [11–13] methods in conjunction with the basis set of 6-31G(d,p) [14]. 3. Results and discussion Picolinic acid on heating with an excess of CH3I is converted into the bis(homarine) hydroiodide (2:1 complex) [6]. In exactly the same conditions, nicotinic acid gave
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103
Fig. 3. Comparison of X-Ray (1) and B3LYP/6-31G(d,p) (2–6) structures.
trigonelline (TRG) hydroiodide (N-methyl-3-pyridiniumcarboxy iodide, 1:1 complex) [15,16]. Hydroiodides are converted into betaines. 3.1. Crystal structure The structure of (HOM)2HÆClO4 with the atom numbering is shown in Fig. 1 and the molecular packing in the crystal in Fig. 2. The bond lengths, bond angles, and torsion angles are listed in Tables 3 and 4. Two molecules of HOM are bridged by a proton to form a homoconjugated cationic system (HOMÆHÆHOM)+ with a short, symmetrical O H O hydrogen bond with the O O distance of ˚ . Because the hydrogen bonded HOM molecules 2.480(3) A are symmetrically equivalent, the (HOM)2H cation is similar to the Type A acid salts of carboxylic acids [17]. In (HOM)2HÆClÆH2O [7], (TRG)2HÆClÆH2O [18], (MIN)2 HÆClÆH2O [19], and bis(quinoline betaine) hydrogen perchlorate [20] H-bonded protons are located asymmetrically, similarly as in the pseudo-Type A acid salts of carboxylic acids. The (HOM)2H cations are arranged approximately parallel in the crystal lattice, as shown in Fig. 2. The carboxy groups participating in the hydrogen bond are planar. The angle between the planes through the rings and COO
groups is 29.98(18). The ClO4 anions are also located symmetrically relative to both positively charged nitrogen atom in HOMÆHÆHOM cations (see Nþ ClO4 distances in Table 4) and the hydrogen bond in the crystal is centrosymmetric. 3.2. B3LYP/6-31G(d,p) calculations Table 4 shows the abbreviations of the molecules investigated, their energies, dipole moments and selected geometrical parameters. In Fig. 3 the crystal linear structure (1) is compared with those optimized by the DFT calculations for isolated units (2–6). There are three important features contributing to the stability of the structures of the molecules in the crystal and the isolated ones (as present in the gas phase): (i) hydrogen bond distance, (ii) electrostatic interactions between the oppositely charged groups and atoms (between the positively charged nitrogen atom with anion and oxygen atoms of COO groups) and (iii) dipole moment. On going from crystal to isolate molecule the inter-molecular (isotropic) electrostatic (Coulombic) attractions disappear but intramolecular (anisotropic) ones become stronger. In consequence the optimized structure of (HOM)2HÆClO4 (2) is different (bent) in comparison with that in the crystal (linear) (1).
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In the optimized (HOM)2H cations (3–6) the hydrogen bonds are shorter in comparison with 1 and 2 (Table 4). In 3 and 4 the N–Me groups, similarly as in 1, are located on the opposite sides of OÆHÆO bridge (t-linear), while in 5 and 6 they are on the same side (c-linear). Their structures are stabilized by the electrostatic interactions between N+ and oxygen atoms. Their relative energies increase with increasing average N+ O distances (Table 4). 3.3. FTIR and Raman spectra In the FTIR spectra of HOMHÆClO4 the mC@O band is at 1744 cm1 (Fig. 4a) and indicates that a proton from the acid is transferred to HOM. The mOH absorption is located in the 3090 cm1 region. The FTIR spectrum of (HOM)2HÆClO4 is dominated by a broad and strong absorption in the range of 1500–400 cm1, typical ˚ . A similar broad of hydrogen bonds shorter than 2.5 A absorption appears in the 2:1 spectra of trigonelline [16], other betaines [21] and type A acid salts of carbox-
Absorbance
2,0
ylic acids [22,23]. This absorption is attributed to the (OHO) stretching and bending vibrations of a short hydrogen bond [24–26]. The continuous absorption and the skeletal vibrations overlap, but the latter feature can be distinguished in the second-derivative spectroscopy, d2 (Fig. 4c). In the second-derivative spectra, the minima have the same wavenumbers as the maxima in the absorption spectra [27], but their intensities vary inversely with the fourth power of the half-width of the absorption bands. The observed wavenumbers in (HOM)2HClO4 and their tentative absorption, based on comparison with the spectrum of HOMHÆCl, are listed in Table 5. In the Raman spectra of the 2:1 complexes the broad absorption is absent (Fig. 4b). The frequency plot of the negative bands in the d2 spectrum versus the Raman frequencies is linear with a unit slope (Fig. 5). Thus the derivative spectrometry can be used to estimate frequencies of the narrow bands covered by the broad absorption due to the stretching and bending OHO vibrations.
a
1,5 1,0 0,5 0,0
Ranam intensity
7,5
b
5,0
2,5
0,0
Arbitrary units
0,2
c
0,0 -0,2 -0,4
3500
3000
2500
2000
1500
1000
500
-1 Wavenumbers (cm ) Fig. 4. Vibrational spectra of (HOM)2HClO4: (a) FTIR (suspension in Nujol and Fluorolube); (b) Raman; (c) second-derivative spectrum; dotted line – FTIR spectrum of HOMHÆClO4.
M. Szafran et al. / Journal of Molecular Structure 839 (2007) 99–106
105
Table 5 Vibrational frequencies of homarine hydrochloride, HOMHÆCl (t), bis(homarine) hydrochloride monohydrate, (HOM)2HClÆH2O and bis(homarine) hydrogen perchlorate, (HOM)2HClO4 HOMHÆCla Raman
3098 3062
(HOM)2HClÆH2Ob FTIR
3092 3082sh 3064 3047sh
Raman
FTIR
3080
3366 3264 3142 3077
3045 3035 3010 2969
3044
2977
3010 2975
1721 1615
2650–2146 1789 1722 1615
1676 1627
1587
1586
1585
1748 1650 1628 1583
1515
1500
1517
1509
1451 1429 1389
1449 1431 1389
1456 1442 1405 1373
1458 1403 1354
1311 1290
1311 1288
1193 1168
1228 1191 1166
1296 1239
1289 1243
1109 1065 1053
1066 1050
913 898
921
813 786
919 898 817 813 772
762
762
762
717 631
723 682 666
686
569
466 449 422 a b
1137
3102 3067
2981
840 829 806
928 915 846 807 791 771
1724 1649 1628 1599 1582 1507 1488 1453 1439 1401 1356 1325 1310 1288
1191 1166 1150 1136
925 912 835 820 791
664
767 744 720 685 668
555
554
575 556
470 442
487 442
722
Approximate assignments FTIR
3143 3101 3088 3063
3142 3102 3086 3061
2981
2981
1742 1622
1741 1621
1582
1584
1583
1509
1509
1454 1431 1403 1376 1345
1455 1430 1402
1286
1286
1171 1165 1094 1085
1170 1145 1096 1081 1068 1052 1027 983 920
1450
1356
1173 1109
1053
932 914 898 839 786
772
733 717 683 631 617 565
695 668 623 560
485 442 429
466 450 422
442
H2O H2O mCH mCH mCH mCH mCH mCH mMe mOH
1686 1619
521
Data from Ref. [6]. Data from Ref. [7]; d2 – second-derivative frequencies.
d2
1500–400
1119 1034
1067 1050
569 534 461 434
3139 3077 3054 3043 3020 3004 2965
Raman
1500–400
1175 1168 1151 1118
1168
(HOM)2HClO4 d2
mCO mCC mCC mCC + mCN bMe + bCH bMe + bCH bMe bMe + bCH bOH bOH
1348
833 804 790 773 760
694 683 624 561 547 526 462 442
bOH mCO + bOH + mCC bCH + mCC + mCN bCH + mCC + mCN bCH + bCN + mCN bMe + bRing + mCO mClO4 + bMe bMe + bCH + bRing mCC + bMe
cCH cCH cCH mCN + bRing bCO + sCO + mCC cCH sCO + sRing sRing + sCC + sCO bRing + bCO
bRing + sRing + bCO bRing + bCO sRing + bCN sRing + cCN sRing
106
M. Szafran et al. / Journal of Molecular Structure 839 (2007) 99–106
References
3000
[1] [2] [3] [4] [5] [6]
2500
d
2
2000 1500
[7]
1000
[8]
500
[9]
500
1000 1500 2000 2500 -1 Raman wavenumbers/cm
3000
[10]
Fig. 5. Relation between d2 and Raman frequencies for (HOM)2HClO4; m(d2) = 4.262 + 1.002 m(Raman), r2 = 0.9998.
4. Conclusions According to the X-ray data, in the crystal of (HOM)2HÆClO4 a pair of homarine molecules are joined by a hydrogen bond involving the proton to form a homoconjugated cation, featuring the short and symmetrical hydrogen ˚ . The bond with the O O distance equal to 2.480(3) A homarine units are equivalent as a result of electrostatic interactions with the ClO4 anion. The ClO4 anions are located symmetrically relative to both positively charged nitrogen atoms in HOMÆHÆHOM cations The COO groups are inclined at 29.98(18) to the plane of the pyridine rings, which are coplanar. The hydrogen bond in (HOM)2HÆClO4 is similar to that in Type A acid salts of carboxylic acids and it can be described by a potential energy function with a single minimum. For the isolated molecule there is no intermolecular (isotropic) electrostatic (Coulombic) attractions characteristic of the crystal structure, but intramolecular (anisotropic) interactions become more important. In consequence, the optimized structure of (HOM)2HÆClO4 (2) is different (bent) than in the crystal (linear) (1). The optimised HOMÆHÆHOM cations, 3–6, are linear with shorter hydrogen bonds relative to that in 1. Their energy decreases with increasing average N+ O distances (Table 4).
Acknowledgement The calculations were performed at the Poznan´ Supercomputing and Networking Centre.
[11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23]
[24] [25] [26] [27]
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