Ab initio and DFT calculations of the structure and vibrational spectra of trigonelline

Article abstract of DOI:10.1016/S0022-2860(02)00250-8

The geometries, frequencies and infrared intensities of the vibrational bands of trigonelline its monohydrate and dimer have been computed by the MP2 and B3LYP approaches using the cc-pVDZ and 6-31G(d,p) basis sets. The computed geometry of the pyridine ring is slightly affected by hydration and dimerization, and satisfactorily agrees with the X-ray data. In contrast, the geometry of the COO group changes significantly on hydration and dimerization. All the measured IR bands were assigned in terms of the calculated vibrational modes. Most computed bands are predicted to lie at higher wavenumbers than the experimental bands. R.M.S. deviation between the experimental and the calculated harmonic frequencies is 69 cm^-1 for all of the bands, and 46 cm^-1 for all bands except those corresponding to v(OH), δ(OH) and v(CH).

Full text of DOI:10.1016/S0022-2860(02)00250-8

Journal of Molecular Structure 614 (2002) 97–108
www.elsevier.com/locate/molstruc
Ab initio and DFT calculations of the structure and vibrational
spectra of trigonelline
*
M. Szafran , J. Koput, Z. Dega-Szafran, M. Pankowski
´
Faculty of Chemistry, Adam Mickiewicz University, ul Grunwaldzka 6, 60780 Poznan, Poland
Received 20 November 2001; revised 25 February 2002; accepted 25 February 2002
Abstract
The geometries, frequencies and infrared intensities of the vibrational bands of trigonelline its monohydrate and dimer have
been computed by the MP2 and B3LYP approaches using the cc-pVDZ and 6-31G(d,p) basis sets. The computed geometry of
the pyridine ring is slightly affected by hydration and dimerization, and satisfactorily agrees with the X-ray data. In contrast, the
geometry of the COO group changes significantly on hydration and dimerization. All the measured IR bands were assigned in
terms of the calculated vibrational modes. Most computed bands are predicted to lie at higher wavenumbers than the
experimental bands. R.M.S. deviation between the experimental and the calculated harmonic frequencies is 69 cm21 for all of
the bands, and 46 cm21 for all bands except those corresponding to n(OH), d(OH) and n(CH). q 2002 Elsevier Science B.V. All
rights reserved.
Keywords: Trigonelline; Geometry; Vibrational spectra; MP2 and DFT calculations
1. Introduction
2. Experimental
2.1. Synthesis
Trigonelline, N-methyl-3-carboxy-pyridine, is a
natural betaine isolated from various plants, seeds
and the western rock lobster [1–5]. Trigonelline
crystallizes as monohydrate and its structure was
determined by X-ray diffraction [5].
Trigonelline hydroiodide. A solution of nicotinic
acid (15 g) in methanol (70 cm3) and methyl iodide
(26 g) was heated at 70 8C in a sealed tube for 40 h.
Yellow crystals were filtered off and washed with
small amount of acetone. The filtrate was evaporated
to dryness under reduced pressure and the solid
residue was washed with acetone. Both fractions of
the crystals were combined and recrystallized from
methanol, total yield 63%, m.p. 235 8C (Ref. [1]
218 8C).
In this paper, the geometry and vibrational spectra
of trigonelline monohydrate (TRGWI–TRGWIII),
anhydrous trigonelline (TRG), and its dimer
(TRGDIM) have been computed by the MP2 and
B3LYP approaches using the cc-pVDZ and 6-
31G(d,p) basis sets.
Trigonelline monohydrate. Trigonelline hydroio-
dide (10 g) was dissolved in water (20 cm3) in a small
canonical flask, propylene oxide (2.6 g) was added
slowly; the flask was closed with a cork and left for 3
*
Corresponding author. Tel.: þ48-61-829-1320; fax: þ48-61-
865-8008.
E-mail address: szafran@main.amu.edu.pl (M. Szafran).
0022-2860/02/$ - see front matter q 2002 Elsevier Science B.V. All rights reserved.
PII: S0022-2860(02)00250-8

98
M. Szafran et al. / Journal of Molecular Structure 614 (2002) 97–108
Table 1
Local-symmetry coordinates of trigonelline and its monohydrate (atom numbering as in Fig. 1)
Symmetry coordinatea
Description
S1 ¼ rN1 –C2
n CN
n CN
n CN
n CC
n CC
n CC
n CC
n CC
n CO
n CO
n CH
n CH
n CH
n CH
S2 ¼ rN1 –C6
S3 ¼ rN1 –C11
S4 ¼ rC2 –C3
S5 ¼ rC3 –C4
S6 ¼ rC4 –C5
S7 ¼ rC5 –C6
S8 ¼ rC3 –C15
S9 ¼ rC15 –O16 þ rC15 –O17
S10 ¼ rC15 –O16 2 rC15 –O17
S11 ¼ rC2 –H7
S12 ¼ rC4 –H8
S13 ¼ rC5 –H9
S14 ¼ rC6 –H10
S15 ¼ rC11 –H12 þ rC11 –H13 þ rC11 –H14
S16 ¼ 2rC11 –H12 2 rC11 –H13 2 rC11 –H14
S17 ¼ rC11 –H13 2 rC11 –H16
n
n
n
s CH3
as CH3
as CH3
S18 ¼ bC6 –N1 –C2 2 bN1 –C2 –C3 þ bC2 –C3 –C4 2 bC3 –C4 –C5 þ bC4 –C5 –C6 2 bC5 –C6 –N1
S19 ¼ 2bC6 –N1 –C2 2 bN1 –C2 –C3 2 bC2 –C3 –C4 þ 2bC3 –C4 –C5 2 bC4 –C5 –C6 2 bC5 –C6 –N1
S20 ¼ bN1 –C2 –C3 þ bC2 –C3 –C4 þ bC4 –C5 –C6 2 bC5 –C6 –N1
S21 ¼ bN1 –C11 –H12 þ bN1 –C11 –H13 þ bN1 –C11 –H14 2 bH12 –C11 –H13 2 bH13 –C11 –H14
2bH12 –C11 –H14
Ring 1
Ring 2
Ring 3
d
s CH3
S22 ¼ 2bH12 –C11 –H13 2 bH13 –C11 –H14 2 bH12 –C11 –H14
S23 ¼ 2bN1 –C11 –H12 2 bN1 –C11 –H13 2 bN1 –C11 –H14
S24 ¼ bH13 –C11 –H14 2 bH12 –C11 –H14
S25 ¼ bN1 –C11 –H13 2 bN1 –C11 –H14
S26 ¼ tC6 –N1 –C2 –C3 2 tN1 –C2 –C3 –C4 þ tC2 –C3 –C4 –C5 2 tC3 –C4 –C5 –C6
þtC4 –C5 –C6N1 2 tC5 –C6 –N1 –C2
S27 ¼ tC6 –N1 –C2 –C3 2 tC2 –C3 –C4 –C5 þ tC3 –C4 –C5 –C6 2 tC5 –C6 –N1 –C2
S28 ¼ 2tC6 –N1 –C2 –C3 2 tN1 –C2 –C3 –C4 þ 2tC2 –C3 –C4 –C5 2 tC3 –C4 –C5 –C6
2tC4 –C5 –C6N1 þ 2tC5 –C6 –N1 –C2
S29 ¼ bC3 –C15 –O16 þ bC3 –C15 –O17
S30 ¼ bC3 –C15 –O16 2 bC3 –C15 –O17
S31 ¼ tC2 –N1 –C11 –H12 þ tC2 –N1 –C11 –H13
þtC2 –N1 –C11 –H14 þ tC6 –N1 –C11 –H12 þ tC6 –N1 –C11 –H13 þ tC6 –N1 –C11 –H14
S32 ¼ tC2 –C3 –C15 –O16 þ tC2 –C3 –C15 –O17
S33 ¼ tC2 –C3 –C15 –O16 2 tC2 –C3 –C15 –O17
S34 ¼ bH7 –C2 –N1
d
as CH3
CH3 wag
as CH3
d
CH3 wag
t ring 1
t ring 2
t ring 3
d
d
s CO2
as CO2
t Me-ring
t CO2
t CO2
b CH
S35 ¼ bH8 –C4 –C3
b CH
S36 ¼ bH9 –C5 –C4
b CH
S37 ¼ bH10 –C6 –C5
b CH
S38 ¼ bC11 –N1 –C2
b CN
S39 ¼ bC15 –C3 –C2
b CC
S40 ¼ gH7 –C2 –N1 –C3
g CH
S41 ¼ gH8 –C4 –C3 –C5
g CH
S42 ¼ gH9 –C5 –C4 –C6
g CH
S43 ¼ gH10 –C6 –N1 –C5
g CH
S44 ¼ gC11 –N1 –C2 –C6
g CN
S45 ¼ tC11 –N1 –C2 –C3
t CC
(continued on next page)

M. Szafran et al. / Journal of Molecular Structure 614 (2002) 97–108
99
Table 1 (continued)
Symmetry coordinatea
Description
Monohydrate
S46 ¼ rO16: –H18
n OH
S47 ¼ rO16· · ·O19
n(OHO)
b OH
S48 ¼ bC15 –O16 –H18
S49 ¼ bO16 –H18 –O19
S50 ¼ gH18 –O16 –C15 –O17
S51 ¼ gO19 –H18 –O16 –C15
S52 ¼ rO19 –H20
b OH
g(OHO)
d(OHO)
n(OH)
g OH
S53 ¼ bH18 –O19 –H20
S54 ¼ gO16 –H18 –O19 –H20
g OH
a
Definitions are made in terms of standard valence coordinates: rij is the bond length between atoms i and j; bijk is the valence angle between
atoms i, j and k, with j the central atom; gijkl is the out-of-plane angle between the i–j bond and the plane defined by the j, k, and l atoms; tijkl is
the torsional (dihedral) angle between the planes defined by the i,j,k and j,k,l atoms.
days. To remove iodopropanols, the reaction solution
was extracted six times with equal volumes of diethyl
ether, then evaporated under reduced pressure to
dryness and the residue was recrystallized from
methanol and white crystals were filtered off, m.p.
218 8C (Ref. [5] 215–217 8C (dec.), Ref. [6] 230–
233 8C); dH 8.88 (s, C2H), 8.61 (1H, m, C6H), 8.58
(1H, m, C4H), 7.83 (1H, dd, C5H, J 6.2, 7.9), 4.20 (3H,
s, N–CH3); dC 168.5 (COO), 146.8 (C6), 146.7 (C2),
145.6 (C4), 137.8 (C3), 128.5 (C5), 49.1 (CH3).
Anhydrous trigonelline was obtained by dehy-
dration of monohydrate in vacuum at 110 8C over
P2O5 for 5 h. The anhydrous trigonelline is very
hygroscopic and converts into the monohydrate when
it is left in open vessel overnight.
2.3. Calculations
The calculations have been performed using the
GAUSSIAN 98 package [7] at the MP2 [8] and B3LYP
[9,10] levels of theory with the basis sets of double-
zeta quality cc-pVDZ [11] and 6-31G(d,p) [12]. The
vibrational IR spectra (the harmonic wavenumbers
and absolute intensities) were calculated only for the
most stable structures.
The harmonic force fields, determined initially in
the cartesian coordinates, were transformed to the
force fields in the internal local-symmetry coordi-
nates. The local-symmetry coordinates, defined in
terms of the internal valence coordinates following
the IUPAC recommendation [13,14] are given in
Table 1. In this way, the redundant internal coordi-
nates were removed. The force fields determined in
this way were used to calculate the harmonic
wavenumbers and vibrational potential energy distri-
bution (PED) among the normal coordinates. PED is
defined as recommended by Keresztury and Jal-
sovszky [15] and calculated with the program
PACK [16,17].
2.2. Spectra
FT-IR spectra were recorded on a Bruker IFS 113v
spectrometer at a 2 cm21 resolution in Nujol and
Fluorolube mulls. Raman spectra were recorded on a
Magna 760 Nicolet operating at the 1064 nm exciting
line of an Nd:YAG laser.
1
The H and 13C NMR spectra were recorded on a
Varian Gemini 300 VT spectrometer operating at
300.07 and 75.46 MHz for proton and carbon-13,
3. Results and discussion
1
respectively. The H and 13C chemical shifts were
measured in D2O solution relative to internal dioxane
and were recalculated relative to TMS by adding 3.55
and 67.40 ppm, respectively. Chemical shifts were
confirmed by COSY, HETCOR and NEODIF
experiments.
3.1. Molecular parameters
The labelling of atoms in TRG·H2O is given in Fig.
1. Some of the possible structures of trigonelline
monohydrate (TRGWXR, TRGWI–TRGWIII) are

100
M. Szafran et al. / Journal of Molecular Structure 614 (2002) 97–108
COO group changes significantly on hydration and
dimerization.
In crystal, the hydrogen atoms of water molecule
bridge to successive O(17) atoms of trigonellines
(TRGWXR, Fig. 2) separated by the z translation;
O(17)· · ·H(A)OH (1 2 x, 2 2 y, 1 2 z) being 2.06(5)
and O(17)· · ·H(B)OH (1 2 x, 2 2 y, 2 2 z) being
˚
1.99(4) A [5]. In the calculated structures (TRGWI–
Fig. 1. Atom numbering for trigonelline monohydrate.
TRGWIII) the water molecule forms one or two
hydrogen bonds with one trigonelline molecule. In the
gas phase, the most stable is TRGWI. The water
molecule forms hydrogen bond to the O(16) atom and
the oxygen atom of the water molecule interacts
electrostatically with the positively charged nitrogen
shown in Fig. 2. The calculated structural parameters,
total energies and dipole moments are collected in
Table 2, together with the X-ray results [5]. The
computed geometry of pyridine ring is only slightly
affected by attaching the water molecule and by
dimerization, and it satisfactorily agrees with the X-
ray data. In contrast, the calculated geometry of the
þ
˚
atom; the N (1)· · ·O(19) distance being 3.940 A and
is remarkably shorter than in TRGWII and TRGWIII.
Fig. 2. Structures of trigonelline monohydrate, anhydrous trigonelline and its dimer.

Table 2
Energies, dipole moments and structural parameters for trigonelline monohydrates, anhydrous and dimer
X-ray
MP2/cc-pVDZ
TRGWI
B3LYP/6-31Gpp
(TRG)
MP2/cc-pVDZ
(TRG)
B3LYP/6-31Gpp
(TRGDIM)
MP2/ccpVDZ
(TRGDIM)
(TRGWXR)
TRGWII
TRGWIII
E (a.u.)
2551.019626 2551.015366 2551.007625 2476.129125
2474.764158
2952.319755
2949.595399
Erel. (kcal/mol)
DE (kcal/mol)
m (Debye)
0
2.7
214.1a
17.5
7.5
29.3a
16.9
216.8a
11.9
238.6b
0.3
242.1b
0.002
1.358
1.360
1.485
1.402
1.402
1.403
1.395
1.556
1.268
1.241
121.7
119.1
119.2
120.3
120.1
118.9
120.4
120.7
119.6
119.4
113.3
115.0
131.7
2179.5
13.8
1.354
15.0
1.357
1.363
1.476
1.398
1.403
1.405
1.396
1.578
1.251
1.246
121.2
120.1
118.7
121.2
119.9
118.4
118.5
123.0
119.6
119.6
112.3
112.7
135.0
180.0
N(1)–C(2)
1.343(5)
1.354(5)
1.480(5)
1.380(4)
1.380(5)
1.383(6)
1.366(5)
1.528(5)
1.253(4)
1.235(4)
120.4(3)
120.5(3)
119.1(3)
121.7(3)
120.3(4)
117.9(3)
119.2(3)
123.0(3)
120.3(3)
119.6(4)
116.8(3)
115.6(3)
127.6
1.357
1.356
1.356
1.355
1.358
1.486
1.393
1.393
1.399
1.380
1.549
1.264
1.239
121.1
119.7
119.1
120.6
120.6
118.7
120.9
120.4
120.0
119.1
114.1
115.1
130.8
179.9
N(1)–C(6)
1.361
1.477
1.401
1.403
1.404
1.395
1.571
1.259
1.242
1.362
1.477
1.398
1.402
1.404
1.396
1.562
1.255
1.250
1.362
1.476
1.398
1.402
1.405
1.396
1.569
1.247
1.253
1.361
1.476
1.386
1.393
1.401
1.381
1.565
1.250
1.243
N(1)–C(11)
C(2)–C(3)
C(3)–C(4)
C(4)–C(5)
C(5)–C(6)
C(3)–C(15)
C(15)–O(16)
C(15)–O(17)
C(2)–N(1)–C(6)
C(2)–N(1)–C(11)
C(6)–N(1)–C(11)
N(1)–C(2)–C(3)
N(1)–C(6)–C(5)
C(2)–C(3)–C(4)
C(2)–C(3)–C(15)
C(4)–C(3)–C(15)
C(3)–C(4)–C(5)
C(4)–C(5)–C(6)
C(3)–C(15)–O(16)
C(3)–C(15)–O(17)
O(16)–C(15)–O(17)
121.8
121.3
121.2
120.6
118.9
119.2
120.8
119.6
118.3
120.7
120.1
119.9
119.6
114.1
113.2
132.7
180.0
120.0
118.7
121.1
119.9
118.6
118.5
122.8
119.5
119.7
112.8
113.3
133.9
180.0
120.1
118.7
121.2
119.9
118.5
118.3
123.2
119.5
119.7
113.1
112.6
134.3
180.0
120.4
119.0
121.4
120.3
118.4
118.6
123.0
119.8
119.4
112.6
113.3
134.2
179.9
C(11)–N(1)–C(2)– 2179.6
C(3)
C(2)–C(3)–C(15)– 2166.6
O(16)
0
0.0
0.0
20.0
0
1.1
20.5
C(2)–C(3)–C(15)–
O(17)
13.3
180.0
180.0
180.0
180.0
180.0
2178.9
179.4
N(1)· · ·O(16)
N(1)· · ·O(17)
N(1)· · ·O(19)
O(16)· · ·H(18)
4.722
4.159
4.074
4.077
4.063
4.740
4.078
4.756
4.136c, 3.443d
4.745c, 5.503d
4.126c, 3.417d
4.759c, 5.464d
4.114
7.260
4.753
3.940
1.740
4.751
6.896
2.084
4.751
7.344
–
(continued on next page)

Table 2 (continued)
X-ray
B3LYP/6-31Gpp
(TRG)
MP2/cc-pVDZ
(TRG)
B3LYP/6-31Gpp
(TRGDIM)
MP2/ccpVDZ
(TRGDIM)
MP2/cc-pVDZ
TRGWI
(TRGWXR)
TRGWII
2.137
TRGWIII
O(17)· · ·H(20)
O(16)· · ·O(19)
O(17)· · ·O(19)
O(16)·H(18)–O(19)
O(17)·H(20)–O(19)
C(15)–O(16)–
H(18)–O(19)
2.363
2.705
164.4
0.0
2.930
2.958
–
2.894
144.6
–
141.6
0.0
114.0
–
C(15)–O(17)–
H(20)–O(19)
20.0
0.0
96.5
O(16)–H(18)–
O(19)–H(20)
2180.0
–
O(17)–H(18)–
O(19)–H(20)
0.0
0.0
a
Interaction energy between trigonelline and water, calculated with E(H2O) ¼ 276.228666 a.u.
b
c
d
Energy of dimerization.
Intramolecular.
Intermolecular.

M. Szafran et al. / Journal of Molecular Structure 614 (2002) 97–108
103
Fig. 3. Comparison of the experimental and calculated spectra of TRG·H2O: (a) the Raman spectrum in the solid state; (b) IR spectrum in Nujol
and Fluorolube emulsion; TRG·D2O dotted line; (c) the IR spectrum predicted at the MP2/cc-pVDZ level of theory.
Structure TRGWII has the water molecule bonded to
both oxygen atoms (O(16) and O(17)) and its energy
is larger by 2.7 kcal/mol. In TRGWIII, the water
molecule is engaged in bifurcated hydrogen bond to
the O(17) atom; both O(17)· · ·H(OH) distances are
in Fig. 3. The broad absorption with maxima at 3414
and 3233 cm21 in the IR spectrum (Fig. 3b) arise from
the stretching vibration of the crystalline water. On
deuteration the bands are shifted to 2526 and
2434 cm21, respectively. In the Raman spectra,
intensity of the O–H stretching frequency is weak
and in TRG·H2O this absorption band is absent (Fig.
3a). In the crystal, two TRG molecules are bridged by
a water molecule forming two (A, B) hydrogen bonds
with the COO groups (see earlier). This explains the
observed absorption shape in the 3400–3150 cm21
region (Fig. 2b). Another interesting feature is the lack
of a typical strong band near 1600 cm21, which is
normally attributed to the antisymmetric COO
stretching mode and its frequency increases very
markedly with the electron-withdrawing effect of
substituent [18]. Four bands in this region are due to
˚
2.363 A. The dimer (TRGDIM, Fig. 2) is stabilized by
an electrostatic interaction between the oppositely
charged nitrogen and oxygen atoms. The dimerization
energy are 238.6 (B3LYP) and 242.1 kcal/mol
(MP2) (Table 2).
3.2. The experimental spectra
TRG·H2O is soluble in water and alcohols and
insoluble in aprotic organic solvents and its vapour
pressure is very low. Therefore, the IR and Raman
spectra were measured in the solid state and are shown

104
M. Szafran et al. / Journal of Molecular Structure 614 (2002) 97–108
Table 3
Observed and calculated (MP2/cc-pVDZ) vibrational frequencies, infrared intensities and potential energy distribution (PED) for trigonelline
monohydrate and anhydrous
TRG·H2O
TRG·D2O
FTIR
TRG
FTIR
nobs
Raman (nobs
)
FTIR
nobs
ncal
PEDa
nobs
ncal
PEDa
ncal
PEDa
3414
3233
3891 (56.4)
3483 (65.7)
3268 (0.1)
S52 99
S47 99
S14 71
2526
2434
2832
2527
3268
S52 98
S47 99
S14 71
S13 26
S12 50
S13 30
S14 20
S12 46
S13 41
S16 90
S17 96
S11 97
S15 99
S10 96
S53 76
S4 23
3268 (0.9)
3253 (6.1)
S14 73
S13 21
S12 44
S13 37
S14 17
S12 53
S13 40
S16 93
S17 100
S11 92
S15 99
S10 97
S
13 26
S12 50
13 30
S14 20
12 46
S13 41
16 90
S17 96
11 97
S15 99
10 96
3255 (6.0)
3244 (2.8)
3255
3244
S
S
3242 (2.5)
3071
3028
3003
2959
1645
1668
1615
3057
3040
3242 (2.8)
3226 (2.0)
3175 (188)
3111 (11.8)
1831 (397)
1741 (59.7)
1683 (2.0)
S
3242
3226
3179
3111
1830
1268
1683
3054
3248 (1.3)
2327 (1.3)
3262 (16.1)
3116 (11.0)
1851 (299)
S
3021
2995
1650
1640
1673
1614
S
1642
1294?
1616
S53 84
S4 23
S7 20
S19 11
S34 10
S6 29
S5 28
S1 11
S34 29
S7 19
S36 12
1621
1680 (3.7)
S4 25
S7 19
S5 14
S19 11
S6 30
S5 26
S1 12
S7 23
S4 22
S2 14
S1 14
S24 34
S22 11
S23 10
S7 20
S19 11
S34 10
S6 29
1583
1580
1506
1630 (2.1)
1581
1506
1630
1533
1584
1625 (1.3)
1526 (8.0)
S5 28
S1 11
1533 (40.2)
S34 29
S7 19
S36 12
1517 (0.4)
S
24 23
1517
1498
S24 23
S2 15
S4 12
S23 10
S7 10
S1 10
S24 29
S22 15
S37 14
1507 (44.3)
1495 (3.53)
S2 15
S4 12
S
23 10
S7 10
S1 10
S24 29
S22 15
1473
1498 (17.8)
1487
S37 22
S36 17
S6 11
S
37 14
S21 10
S22 67
S24 23
1461
1429
1457
1425
1492 (12.8)
1453 (1.3)
S22 66
1458
1492
1453
S22 66
1488 (12.7)
1449 (5.6)
S
25 10
S24 35
S1 22
S2 12
S24 35
S1 22
S24 24
S2 17
S2 13
S1 15
1446 (0.7)
1347 (4.0)
S
21 86
1446
1347
S21 87
S34 41
S35 21
S36 16
1443 (0.7)
S21 90
S37 21
S34 18
S35 16
1319
1321
S34 41
S35 21
1322
1309
1289 (23.3)
S
36 16
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M. Szafran et al. / Journal of Molecular Structure 614 (2002) 97–108
105
Table 3 (continued)
TRG·H2O
TRG·D2O
FTIR
TRG
FTIR
nobs
FTIR
Raman (nobs
)
nobs
ncal
PEDa
nobs
ncal
PEDa
ncal
PEDa
S3 12
S36 10
S9 84
1364
1219
1367
1217
1334 (238)
1262 (36.6)
S9 85
S29 10
S3 36
S37 20
S18 13
S2 12
S1 10
S37 21
S7 15
1370
1217
1334
1261
S9 84
S29 10
S3 34
S37 17
S18 13
S2 10
1377
1361
1218
1308 (203)
1239 (24.3)
S3 26
S18 19
S34 17
1201
1196
1153
1194 (0.4)
1197
1153
1194
S37 22
S7 15
1189 (1.0)
S36 27
S37 26
S7 20
S
35 13
S35 12
S36 10
S36 26
S23 16
S5 10
1170 (13.5)
1150 (0.9)
1128 (2.8)
S
36 28
1168
1150
1128
1176
1114
1145 (0.1)
1125 (17.2)
1115 (28.4)
S25 86
S23 16
S5 10
S25 81
S25 81
S23 45
S
35 18
S34 12
S34 28
S36 18
S6 15
1134
1134
S
23 34
S35 15
36 14
1134
S23 34
S35 15
S36 15
S6 14
S
S6 14
S8 10
1089
1030
1080 (8.0)
1055 (2.7)
1032 (2.3)
999 (2.0)
929 (2.2)
909 (44.0)
S35 29
1073
1032
1080
1053
1031
998
S35 29
S23 21
S6 12
1080
1028
1073 (12.1)
1008 (0.0)
1033 (2.7)
941 (0.9)
S35 27
S23 25
S
23 21
S6 12
1030
S40 88
S40 87
S41 14
S41 75
S42 35
S
41 13
S18 45
S18 45
S18 48
S6 11
S7 10
981
913
857
987
909
857
S41 59
S42 43
987
909
857
S41 58
S42 43
S40 14
S42 39
S43 39
S41 24
S3 29
S42 43
S40 40
S43 24
S40 58
S4117
S43 14
S3 29
S
40 12
S42 39
S43 39
927
906
843
910 (9.5)
S
41 24
S3 29
S8 20
909
898 (28.0)
S8 20
S8 18
S
19 15
S19 15
S19 17
S
18 10
585
784
854 (319)
810 (11.6)
S49 65
S54 15
S43 54
487
782
620
810
S49 67
S54 15
S43 54
S33 23
S42 10
S29 60
805 (14.2)
777 (95.6)
S43 59
S33 21
S42 10
S29 66
S
33 22
S42 11
29 59
789
787 (90.4)
S
787
781
768
S
20 10
(continued on next page)

106
M. Szafran et al. / Journal of Molecular Structure 614 (2002) 97–108
Table 3 (continued)
TRG·H2O
TRG·D2O
FTIR
TRG
FTIR
nobs
FTIR
Raman (nobs
)
nobs
ncal
PEDa
nobs
ncal
PEDa
ncal
PEDa
691
694
756 (46.5)
S33 49
S43 13
S42 13
693
756
S33 49
S43 14
S42 13
751 (37.1)
S33 52
S43 12
S42 12
S41 10
S20 68
S29 16
S26 107
S19 48
S30 20
S3 10
681
557
689 (8.8)
S
20 66
680
558
691
S20 65
S29 14
S26 103
S19 46
S30 21
688
678
553
686 (7.5)
S29 15
S26 104
S19 45
553
516
675 (4.0)
552 (0.9)
675
552
670 (1.9)
548 (0.2)
S
30 21
514
466
498 (5.8)
459 (7.9)
S
S
30 31
19 21
515
496
459
S30 32
S19 20
S39 14
S44 36
S27 35
S26 11
S28 11
S51 116
S49 26
S53 10
510
494 (5.4)
S30 40
S19 17
S39 14
S27 36
S44 36
S28 13
S26 11
S39 14
27 38
S44 36
S
456 (4.24)
S
26 12
436 (20.1)
400 (46.6)
S
28 55
428
303
425
S51 50
32 14
S49 10
S
399
372
S
S
51 74
28 28
S28 79
S27 16
S32 13
414 (0.0)
S28 85
S27 19
S49 14
27 10
S
385 (2.7)
344 (8.4)
S38 47
S30 25
385
344
S38 47
S30 25
S8 10
381 (0.7)
330 (6.0)
S38 54
S30 17
S8 42
S8 41
S8 48
S
S
38 13
19 10
S38 14
S19 10
S38 11
S19 11
S18 10
296 (64.7)
S54 121
S50 20
211
S54 84
S50 19
S46 18
S27 12
S54 39
S46 31
S27 35
S44 32
S46 11
S48 66
S45 35
S51 13
S45 28
S39 24
S46 21
S48 15
S39 29
224
172
227 (33.6)
213 (3.7)
S46 71
226
212
S
S
39 14
27 44
213 (2.1)
S44 42
S27 39
S28 10
S44 40
160 (7.6)
150 (0.7)
S
48 64
157
148
S45 37
S51 10
S39 28
143 (2.3)
171 (4.2)
S45 90
S
45 27
S46 19
S
S
48 16
39 28
114
119 (13.4)
117
S39 70
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M. Szafran et al. / Journal of Molecular Structure 614 (2002) 97–108
107
Table 3 (continued)
TRG·H2O
TRG·D2O
FTIR
TRG
FTIR
nobs
FTIR
Raman (nobs
)
nobs
ncal
PEDa
nobs
ncal
PEDa
ncal
PEDa
S45 17
S45 15
S51 13
S30 12
S31 83
S32 10
S32 62
S50 33
S27 10
S50 61
S32 21
S48 10
S30 14
S31 92
S
30 11
S51 11
S31 83
101 (1.4)
66 (0.3)
101
66
17 (0.0)
72 (0.0)
S
32 10
S32 61
S50 34
S27 10
S32 90
S27 17
43 (2.5)
46b, 69c
S
50 63
43
S32 22
S48 11
R.M.S.
61b, 85c
a
Only contributions greater than 10 are listed.
b
c
R.M.S. error for bands (without nOH, dOH, gOH and nCH modes).
R.M.S. error for all bands.
strongly coupled in-plane bending vibrations of the
water molecule, COO stretching, and ring stretching
frequencies. The band at 1673 cm21 is absent in the
spectrum of anhydrous trigonelline and it is shifted to
1455 cm21 when H2O is replaced by D2O (Fig. 2b).
Thus, this band corresponds to the bending mode of
the water molecule. The bands at 1640 and 1367 cm21
are due to the antisymmetric and symmetric COO
stretching vibrations, respectively.
may be responsible for the discrepancy between the
experimental and computed spectra of TRGWI. The
first is that the experimental spectrum is for the
complex in the crystal, whereas the computed one
refers to the isolated complex in the gas phase. For the
real crystal structure, both hydrogen atoms of the
water molecule are engaged in hydrogen bonds, while
only one hydrogen atom in the computed structure.
Therefore, the calculated frequencies of the vOH and
dOH vibrations are overestimated. The second reason
for this discrepancy is the fact that the experimental
values are anharmonic frequencies while the calcu-
lated values are harmonic frequencies. For the skeletal
modes, the difference between the experimental and
calculated frequencies are much smaller than those for
H2O. R.M.S. deviation between the experimental and
calculated harmonic frequencies are 69 cm21 for all
bands and 46 cm21 for all bands except the n(OH),
d(OH) and n(CH) ones. The MP2 method reproduces
correctly the isotope frequency ratio, n H/nD.
3.3. The computed IR spectra and interpretation of the
experimental spectrum
For the most stable structure of trigonelline
monohydrate, TRGWI, the intramolecular
þ
˚
N(1) · · ·O(19) distance is predicted to be 3.940 A,
which is significantly shorter than that found in the
˚
crystal (7.260 A) [5]. In the crystal, the unit cell
contents a pair of TRG molecules together with two
water molecules. Thus in the crystal, the charged
nitrogen atom interacts electrostatically with the
oxygen atoms from the neighbouring COO2 groups
and the water molecules.
4. Conclusions
Table 3 lists the calculated harmonic frequencies,
intensities, and PEDs for normal modes. A compari-
son of the calculated and experimental frequencies
shows substantial differences, especially for the
frequencies assigned to water vibrations. Two factors
The structural parameters, harmonic frequencies
and IR intensities of the vibrational bands were
calculated at the MP2 and B3LYP levels of theory
using cc-pVDZ and 6-31G(d,p) basis sets. The

108
M. Szafran et al. / Journal of Molecular Structure 614 (2002) 97–108
J.B. Saunders, B.W. Skelton, A.H. White, Aust. J. Chem. 34
(1981) 787.
predicted frequencies were compared with the
experimental data in the solid state. The computed
geometry of the pyridine ring is slightly affected by
hydration and dimerization, and satisfactorily agrees
with the X-ray data. As expected, the geometry of the
COO group changes significantly on hydration and
dimerization. A satisfactory reproduction of the
experimental frequencies, except that of the modes
for the water unit, is obtained. The differences for the
nOH and nCH stretches are consistent with the
expected anharmonicity of 170–200 cm21 for these
modes.
[6] E.M. Kosover, J.W. Patton, J. Org. Chem. 26 (1961) 1318.
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Acknowledgments
The authors are grateful to Professor W.B. Person
for providing of the PACK program and stimulating
discussion. Calculations were performed at the
Poznan Supercomputing and Networking Centre.
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