Intramolecular H?H Interactions for the Crystal Structures of [4-((E)-But-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate and [4-((E)-Pent-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate; DFT Calculations on Modeled Styrene Derivatives

Article abstract of DOI:10.1021/jp0351829

The crystal and molecular structures of [4-((E)-but-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate (BDMP) and [4-((E)-pent-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate (PDMP) are investigated by low-temperature X-ray diffraction measurements. The geometries of these molecules indicate that intramolecular dihydrogen bonds may exist for these structures. The use of the Bader theory supports this statement. To analyze the nature of such interactions, model calculations on styrene and its derivatives have been performed at B3LYP/6-311++G** level of theory.

Full text of DOI:10.1021/jp0351829

J. Phys. Chem. B 2004, 108, 1831-1837
1831
Intramolecular H‚‚‚H Interactions for the Crystal Structures of
[4-((E)-But-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate and
[4-((E)-Pent-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate; DFT Calculations on
Modeled Styrene Derivatives
Sławomir J. Grabowski,*,† Arno Pfitzner,*,‡ Manfred Zabel,‡ Alina T. Dubis,§ and
Marcin Palusiak†
Department of Crystallography and Crystal Chemistry, UniVersity of Ło´dz´,
90-236 Ło´dz´, ul. Pomorska 149/153, Poland, Institut fu¨r Anorganische Chemie der UniVersita¨t Regensburg,
93040 Regensburg, Germany, and Institute of Chemistry, UniVersity of Białystok, Al. J. Piłsudskiego 11/4,
15-443 Białystok, Poland
ReceiVed: May 2, 2003; In Final Form: October 28, 2003
The crystal and molecular structures of [4-((E)-but-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate
(BDMP) and [4-((E)-pent-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate (PDMP) are investigated by
low-temperature X-ray diffraction measurements. The geometries of these molecules indicate that intramolecular
dihydrogen bonds may exist for these structures. The use of the Bader theory supports this statement. To
analyze the nature of such interactions, model calculations on styrene and its derivatives have been performed
at B3LYP/6-311++G** level of theory.
Introduction
correlation between the H-bond energy and the elongation of
the proton donating bond due to the dihydrogen bond forma-
tion.13,14 The nature, the structure, and energetic characteristics
of dihydrogen bonds were extensively studied,15,16 the topologi-
cal analysis based on the Bader theory17 was also applied.14,18-20
The theoretical evidence of the existence of intramolecular
dihydrogen bonds has been described21,22 and it was also
detected that for some of such intramolecular systems there is
the π-electron delocalization which exists for the so-called
resonance assisted hydrogen bonds (RAHBs).23,24
The blue-shifting hydrogen bonds were detected for some
C-H‚‚‚Y systems for which there is no typical elongation of
the donating bond connected with the normal red shift of the
C-H stretch frequency but a blue shift is observed connected
with the decrease of the C-H bond length.12
The aim of the present study is to analyze the crystal
structures of [4-((E)-but-1-enyl)-2,6-dimethoxyphenyl]pyridine-
3-carboxylate (BDMP) and [4-((E)-pent-1-enyl)-2,6-dimethoxy-
phenyl]pyridine-3-carboxylate (PDMP) because in such struc-
tures intramolecular H‚‚‚H contacts exist that might be treated
as dihydrogen bonds. Additionally, these compounds are
important due to their biological activity; such activities were
detected during studies on R-asarone derivatives.
R-Asarone is the principle active component of the bark
extract of Guatteria gaumeri25 and Acorus calamus.26 These
extracts have been used traditionally to prevent elevation of
plasma lipids. Earlier works27,28 suggest that some of the
R-asarone derivatives could be effective hypolipidaemic agents.
A detailed 1H NMR study of a series of R-asarone isomers was
also made.29 Furthermore, the crystal structures of 1,2,5-
trimethoxy-3-(1-propenyl)benzene and 1,3,5-trimethoxy-2-(1-
propenyl)benzene have been determined by X-ray diffraction
methods.30 In both cases existence of the intra- and intermo-
lecular C-H‚‚‚O hydrogen bonds was observed.
Hydrogen bonding is one of the most important interactions
influencing the arrangement of molecules in crystals and having
a dominant role for their physical properties.1-5 The problem
of this interaction is connected with the fact that the definition
and the criteria of existence of hydrogen bonding are not
unequivocal. Early works claim that an H-bond, often designated
as X-H‚‚‚Y, exists between the proton donating X-H bond
and the proton acceptor Y usually containing at least one lone
electron pair; the hydrogen atom of the X-H bond should be
positively charged and the Y-accepting center should have the
excess of electron charge.6 Early works report that for such
X-H‚‚‚Y interactions X and Y should be electronegative atoms.
However, there are so-called unconventional hydrogen bonds
with X or Y being carbon atoms; these are C-H‚‚‚Y or X-H‚
‚‚C interactions or hydrogen bonds with π-electrons as the
proton acceptors.4 Such unconventional H-bonds early on
described and found in crystal structures7 have been commonly
admitted after the appearance of the work of Taylor and Kennard
where the statistical justification of the existence of hydrogen
bonds with C-H donating bonds based on the data taken from
Cambridge Structural Database (CSD)8 was given.9 The problem
is more complicated because other kinds of hydrogen bonds
were detected in past decade; among them are dihydrogen
bonds10,11 and blue-shifting hydrogen bonds.12
A dihydrogen bond was defined as that one for which the
typical X-H proton donating bond exists and the weak base
component is a metal hydride or B-H bond.10,11 It was pointed
out that a dihydrogen bond is similar to typical, conventional
hydrogen bonding. For example, a correlation between the
H-bond energy and the H‚‚‚H distance was found or a
† University of Ło´dz´.
‡ Institut fu¨r Anorganische Chemie der Universita¨t Regensburg.
§ University of Białystok.
10.1021/jp0351829 CCC: $27.50 © 2004 American Chemical Society
Published on Web 01/14/2004

1832 J. Phys. Chem. B, Vol. 108, No. 6, 2004
Grabowski et al.
TABLE 1: Crystallographic Data and Structure Refinement
Experimental Section
1
2
Melting points were determined on a Mettler DSC30 in
1
aluminum sample containers. H and 13C NMR spectra were
formula
M
crystal system
space group
a (Å)
b (Å)
c (Å)
C18H19NO4
313.34
monoclinic
P21/c
9.0694(7)
22.470(2)
8.1591(6)
97.872(9)
1647.1(2)
4
C19H21NO4
327.37
monoclinic
P21/c
8.9277(6)
23.583(1)
8.1672(5)
98.186(8)
1702.0(2)
4
recorded on a Bruker AC 200F spectrometer using CDCl3
solution with TMS as internal standard (chemical shifts in δ
ppm). IR spectra were recorded on a Nicolet Magna 550 FTIR
spectrometer in chloroform solutions. Column chromatography
was performed using Merck Kieselgel 60, 70-230 mesh. Thin-
layer chromatograms were developed on aluminum TLC sheets
precoated with silica gel F254. The spots were visualized with
50% sulfuric acid after heating. All the solvents were dried and
freshly distilled prior to use.
â (deg)
V (Å3)
Z
Dx (g cm-3
)
1.264
0.089
173(1)
1.278
0.090
173(1)
µ (mm-1
T (K)
)
Synthesis. 1-Bromoalkane (0.1 mol) in 20 mL of THF was
added dropwise to the mixture of 2.4 g (0.1 mol) of magnesium
turnings in 15 mL of dry THF. The solution of 3.64 g (0.02
mol) of 3,5-trimethoxy-4-hydroxybenzaldehyde in 50 mL of
THF was cooled to -70 °C (dry ice-acetone bath) and
magnesium alkylbromide (propyl or butyl, respectively) was
added. After 10 min the ice bath was removed. The reaction
mixture was stirred 2 h at room temperature. After completion
of the reaction (TLC control) the mixture was quenched with
50 mL of methanol and water and product was extracted with
ether. The organic extract was washed with water and dried
over magnesium sulfate and evaporated. The resulting 4-(hy-
droxyalkyl)-2,6-dimethoxyphenol was subjected to the next step.
A solution of the crude alcohol (0.02 mol) in 50 mL of dry
toluene was treated with 4.8 g (0.03 mol) of CuSO4.31 The
reaction mixture was refluxed for 2 h. An inorganic material
was filtered off and washed with toluene. The solvent was
removed, yielding the crude alkene, which was purified by silica
gel column chromatography. Elution with hexane/ether; 7:3 (v/
v), yielded 0.01 mol of 4-((1E)-but-1-enyl)-2,6-dimethoxyphenol
or 4-((1E)-pent-1-enyl)-2,6-dimethoxyphenol.
A solution of 0.01 mol of 4-((1E)-alkyl-1-enyl)-2,6-dimeth-
oxyphenol in 15 mL of dry pyridine was treated under inert
gas (argon) with 0.056 mol of nicotinoyl chloride hydrochloride.
The reaction mixture was heated overnight at 50 °C with
catalytic amounts of 4-(dimethylamino)pyridine (DMAP). After
cooling, the reaction mixture was poured into a cold solution
of ammonium chloride and extracted twice with chloroform.
After evaporation of the solvent the residue was purified by
silica gel column chromatography (elution with hexane/ether;
1:1; v/v). The nicotinic acid ester was crystallized from ethanol/
hexane to give the pure product as a white needle (0.005 mol,
50% yield).
λ (Å)
0.71073
-11 e h e 11
-27 e k e 27
-10 e l e 9
12753
3132
0.0531
2314
284
0.0485
0.0851
0.71073
-10 e h e 10
-26 e k e 28
-9 e l e 10
12544
3244
0.0632
2527
294
0.0682
0.1633
index ranges
no. of data collected
no. of unique data
Rint
no. of I > 2σ(I) data
no. of parameters
R1 (all data)
wR2 (all data)
R1 [I > 2σ(I)]
wR2 [I > 2σ(I)]
0.0325
0.0801
-0.129
0.181
0.0555
0.1545
-0.292
0.839
∆Fmin (e Å-3
)
∆Fmax (e Å-3
)
(CH), 152.1 (C), 151.5 (CH), 137.6 (CH), 136.7 (C), 131.5 (CH),
129.6 (CH), 127.3 (C), 125.4 (C), 123.2 (CH), 102.5 (CH), 56.01
(CH3), 34.93 (CH2), 22.3 (CH2), 13.6 (CH3). MS (M + H)+ )
328.
X-ray Measurements. Transparent, colorless crystals of each
compound, mounted on glass fiber, were used for diffraction
measurement. The data were collected on a STOE IPDS imaging
plate single-crystal diffractometer32 with a low-temperature
device, using Mo KR source and a graphite monochromator.
Data reduction was performed with the STOE IPDS-software
package.32 The Lorentz and polarization corrections were
applied. Cell parameters were determined by indexing of 8000
reflections with I/σ(I) > 6.0.
The structures were solved by direct methods using SIR-9733
and refined by full-matrix least-squares methods on F2 using
SHELXL97.34 All non-hydrogen atoms were refined with
anisotropic thermal displacement parameters. Hydrogen atoms
were located geometrically using AFIX in SHELXL97.34 At
the final stage of both structure refinements all H-atoms, except
for H61(C60) and H62(C60) of the PDMP molecule, were fully
refined with isotropic thermal displacements. The positions of
H61(C60) and H62(C60) atoms were left according to AFIX
location. Molecular geometries were calculated by PARST.35
Graphical presentation of molecules was performed using
PLATON.36
The crystal data and details of the X-ray analysis are given
in Table 1. It has to be stated that the quality of the PDMP
crystals was significantly lower than that of the BDMP crystals.
This becomes immediately obvious from the data in Table 1.
Crystallographic data for the structural analysis have been
deposited with the Cambridge Crystallographic Data Centre;
No. CCDC 212706 and No. CCDC 212707.
[4-((E)-But-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-car-
boxylate. Mp: 127 °C (decomposition). IR (CHCl3), ν (cm-1):
1746, 1597, 1508, 1420, 1352, 1327, 1279,1134, 1090, 1023,
1
964, 853. H NMR (200 MHz, CDCl3), δ: 9.42 (s, 1H, ArH),
8.84 (dd, 1H, ArH), 8.44 (m,1H, ArH), 7.43 (m, 1H, ArH), 6.64
(s, 2H, ArH), 6.43 (m, 1H, CHd), 6.32 (m, 1H, dCH), 3.81 (s,
6H, -OCH3), 2.24 (dt, 2H, -CH2), 1.10 (t, 3H, CH3). 13C
NMR: δ 163.2 (C), 153.6 (CH), 152.0 (C), 151.5 (CH), 137.6
(CH), 136.7 (C), 133.1 (CH), 128.5 (CH), 127.2 (C), 125.0 (C),
123.2 (CH), 102.5 (CH), 55.9 (CH3), 25.8 (CH2), 13.4 (CH3).
MS (M + H)+ ) 314.
[4-((E)-Pent-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-car-
boxylate. Mp: 117 °C (decomposition). IR (CHCl3), ν (cm-1):
1746, 1597, 1508, 1463, 1420, 1329, 1327, 1279, 1134, 1091,
1
1023, 964, 842. H NMR (200 MHz, CDCl3), δ: 9.42 (s, 1H,
Computational Details
ArH), 8.84 (dd, 1H, ArH), 8.48 (dt, 1H, ArH), 7.44 (m, 1H,
ArH), 6.64 (s, 2H, ArH), 6.32 (m, 1H, CHd), 6.24 (m, 1H,
dCH), 3.81 (s, 6H, -OCH3), 2.18 (dt, 2H, -CH2), 1.50 (m,
2H, CH2), 0.96 (t, 3H, CH3). 13C NMR: δ 163.2 (C), 153.6
The calculations have been performed using the Gaussian98
set of codes.37 The B3LYP method is applied; this method is a
hybrid density functional theory approach that combines Becke’s

Crystal and Molecular Structures of BDMP and PDMP
J. Phys. Chem. B, Vol. 108, No. 6, 2004 1833
three-parameter nonlocal exchange potential38 with the nonlocal
correlation functional of Lee, Yang, and Parr.39 The 6-311++G**
basis set was applied because the inclusion of the diffuse
components in the basis set is desired to describe properly the
hydrogen bonding interaction.5 In other words, the B3LYP/
6-311++G** level of theory was applied for all calculations
performed here. The wave functions obtained were used with
the AIM2000 program40 (based on the Bader theory17) to
calculate the topological properties of the systems under
investigation. Hence the critical points (CPs) may be localized,
and their properties such as electron densities at CPs and their
Laplacians may be analyzed.
TABLE 2: Possible Hydrogen Bonds (Bonds and Distances
in Ångstroms and Angles in Degrees) for Structures of
1 and 2
donor-H donor‚‚‚acceptor H‚‚‚acceptor donor-H‚‚‚acceptor
For 1
C1-H1
0.96(0.02)
1.08
C3-H3
0.98(0.02)
1.08
C1‚‚‚O21(0)a
H1‚‚‚O21(0)
2.58(0.01)
2.57
H3‚‚‚O20(0)
2.42(0.01)
2.41
C1-H1‚‚‚O21(0)
2.875(0.001)
97.8(0.9)
95.2b
C3‚‚‚O20(0)
2.722(0.001)
C3-H3‚‚‚O20(0)
97.4(0.9)
95.0b
C23-H23
0.97(0.01)
1.08
C23‚‚‚N1(1)
3.703(0.002)
H23‚‚‚N1(1)
2.77(0.01)
2.67
C23-H23‚‚‚N1(1)
161.4(1.1)
160.7b
In this study the single point B3LYP/6-311++G** calcula-
tions have been performed on [4-((E)-but-1-enyl)-2,6-dimeth-
oxyphenyl]pyridine-3-carboxylate (BDMP) and [4-((E)-pent-1-
enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate (PDMP)
molecules for geometries taken from the X-ray measure-
ment; only the neutron diffraction corrections for C-H
bond were done before calculations.41,42 Further, the obtained
B3LYP/6-311++G** wave functions of BDMP and PDMP
were applied for the topological analysis. There are the
CdCsH‚‚‚HsC(benzene ring) H‚‚‚H contacts within BDMP
and PDMP, and hence the calculations were also performed for
the modeled systems where similar contacts exist. The calcula-
tions have been performed for styrene and its fluorine deriva-
tives, and the Bader theory was also used to analyze the
intramolecular interactions.
C40-H40
0.96(0.02)
1.08
C25-H25
0.98(0.02)
1.08
C40‚‚‚N1(1)
H40‚‚‚N1(1)
2.69(0.02)
2.57
H25‚‚‚O26(2) C25-H25‚‚‚O26(2)
2.65(0.02)
2.56
C40-H40‚‚‚N1(1)
159.9(1.5)
159.0b
3.600(0.002)
C25‚‚‚O26(2)
3.535(0.002)
150.3(1.2)
149.2b
For 2
C1-H1
0.97(0.03)
1.08
C3-H3
0.95(0.02)
1.08
C1‚‚‚O21(0)
2.871(0.002)
H1‚‚‚O21(0)
2.56(0.02)
2.54
H3‚‚‚O20(0)
2.47(0.02)
2.46
C1-H1‚‚‚O21(0)
99.0(1.6)
96.5b
C3‚‚‚O20(0)
2.721(0.002)
C3-H3‚‚‚O20(0)
95.1(1.5)
92.0b
a Equivalent positions denoted in parentheses: (0) x, y, z; (1) x - 1,
+y, +z - 1; (2) x, -y + 1/2 + 1, +z - /2. b C-H distances were
1
normalized by moving the position of the H-atom along the C-H
vector.
Results and Discussion
FTIR and NMR Spectra. The FTIR spectra of [4-((E)-but-
1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate and [4-((E)-
pent-1-enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate re-
vealed a strong absorption of the carbonyl group at 1746 cm-1
.
This position and intensity is typical for esters. An additional
intense band at 1279 cm-1 due to the CsO stretching vibration
in esters is also observed in both spectra. The ether CsO
stretching bands appear at 1134, 1092, and 1091 cm-1. The
presence of unsaturation in the molecules is recognized by the
presence of a sharp band at 1597 cm-1. It is worthy of note
that the CdC bond in the butenyl and pentenyl chain is
conjugated with an aromatic ring. As a consequence the CdC
bond has less double-bond character and the absorption band
νCdC is shifted to lower wavenumbers in comparison with simple
alkenes. Additionally, the band at 964 cm-1 is due to the CsH
out-of plane bending vibration of hydrogen atoms attached to
unsaturated carbon and is consistent with a trans substitution
pattern. The 1H NMR spectrum also exhibits a trans arrangement
of the olefinic protons. The chemical shift values of the hydrogen
atoms attached to the unsaturated carbon atoms are 6.43 (6.24)
and 6.32 ppm and the coupling constant is J12 ) 15.8 Hz.
Crystal and Molecular Structures. Table 2 shows the
possible intramolecular and intermolecular hydrogen bonds.
Table 2 shows only those contacts for which the proton‚‚‚
acceptor distances are shorter than the corresponding sum of
van der Waals radii. We see that there are only a few such
intermolecular and intramolecular contacts for the structure of
BDMP, whereas for the structure of PDMP there are only
intramolecular contacts that may be treated as hydrogen bonds.
For both crystal structures intramolecular C-H‚‚‚O contacts
are detected, such a situation was also observed previously for
the crystal structure of ethyl 3,4,5-trimethoxybenzoate (ET-
MB).43 However, to study those intramolecular interactions only
the geometrical parameters were aanalyzed.43 For benzene
derivatives the possibility of the existence of intramolecular
Figure 1. Molecular structures of BDMP and PDMP with atom
labeling scheme. The displacement ellipsoids are drawn at 50%
probability level.
H-bonds between substituents and C-H donors being in ortho
positions, according to them, is the additional problem that needs
explanation. It will be considered in detail in the next section
describing the results of ab initio calculations. Such a situation
was observed for ETMB and also for BDMP and PDMP crystal
structures (C1-H1‚‚‚O21 and C3-H3‚‚‚O20 contacts; see
Figure 1).
Figure 1 shows for both structures the intramolecular H‚‚‚H
contacts (dotted lines); the H‚‚‚H distances amount to 2.20 and
2.17 Å for BDMP and PDMP respectively. This kind of
interaction is also described in the next section in detail.
DFT and AIM Calculations for BDMP and PDMP
Molecules. Figures 2 and 3 present the molecular graphs of

1834 J. Phys. Chem. B, Vol. 108, No. 6, 2004
Grabowski et al.
Figure 2. Molecular graph of BDMP. The positions of atoms, BCPs, and RCPs are given.
Figure 3. Molecular graph of PDMP. The positions of atoms, BCPs, and RCPs are given.
BDMP and PDMP, respectively. These graphs were obtained
from the B3LYP/6-311++G** wave functions after the use of
the AIM2000 program. The calculations have been performed
for geometries taken from crystal structures. The C-H bond
lengths have been corrected because it is well-known that X-ray
diffraction methods do not reflect properly the X-H bond
lengths. The positions of atoms are determined from the electron
density maxima and hence the errors are mainly connected with
positions of hydrogen atoms. The neutron diffraction measure-
ments deliver the proper atomic positions for all atoms
considered. In the case of results of X-ray measurements it is
common to correct the hydrogen atom positions; C-H bonds
are fixed to be 1.083 Åsan average value for C-H bond length
obtained from spectroscopy and neutron diffraction measure-

Crystal and Molecular Structures of BDMP and PDMP
J. Phys. Chem. B, Vol. 108, No. 6, 2004 1835
ments.4 Hence C-H distances were normalized in the present
work by moving the position of the H atom along the C-H
vector to the fixed value of 1.083 Å.
CHART 1: Styrene and Its Derivatives (X,Y ) H,H,
F,H, H,F, and F,F)
We see that the application of the Bader theory indicates the
bond path between the hydrogen atoms and there are the bond
critical points (BCPs) for such interactions (Figures 2 and 3).
This may suggest that intramolecular dihydrogen bonds exist
for BDMP and PDMP molecules. We also see that there are no
bond paths for C-H‚‚‚O intramolecular contacts similar to those
described earlier for ETMB43 as intramolecular hydrogen bonds.
Hence the use of the Bader theory may be treated as a decisive
tool for the characterization of the type of interaction because
the geometrical criteria are not decisive if H-bonds exist.
The above-mentioned H‚‚‚H contacts were analyzed in terms
of electron density. For BDMP the electron density at the H‚‚
‚H bond critical point is equal to 0.0105 au whereas for PDMP
it is 0.0112 au. The corresponding Laplacians of these densities
are equal to 0.0396 and 0.0419 au, respectively. It is well-known
that the electron density at the H-bond BCP may be treated as
the measure of the hydrogen bond strength.44-46 The topological
criteria of hydrogen bonding have been given by Koch and
Popelier.47,48 According to them the BCP and the bond path
should exist for an X-H‚‚‚Y hydrogen bond; the electron
density and its Laplacian for an H‚‚‚Y contact should be within
the ranges 0.002-0.04 au for the electron density and 0.02-
0.15 au for its Laplacian. We see that both H‚‚‚H interactions
for BDMP and PDMP fulfill these criteria. We may conclude
that those intramolecular dihydrogen bonds are of medium/
weaker strength; for example, for the linear (trans) water dimer
the electron density at H‚‚‚O BCP is equal to 0.023 au for the
B3LYP/6-311++G** level of theory49 for which the H-bond
energy is about 5 kcal/mol. It may suggest that the intramo-
lecular dihydrogen bond energy is in the range 2-3 kcal/mol.
It is worth mentioning that the topological parameters are
insensitive to the level of calculation; for example, for the same
linear (trans) dimer of water the electron density at H‚‚‚O BCP
is equal 0.024 au if the MP2/6-311++G** level is applied.49
For intramolecular H-bonds the properties of ring critical points
(RCPs) may be also treated as measures of H-bond strength.50,51
The electron densities for RCPs of BDMP and PDMP amount
to 0.0102 and 0.0107 au, respectively, and the corresponding
values of Laplacians are equal to 0.0508 and 0.0542 au. For
comparison, for the RCP created due to the formation of
intramolecular H-bond for malonaldehyde the electron density
at RCP is equal 0.0205 au and its Laplacian to 0.1277 au, for
the MP2/6-311++G** level of calculation. The roughly
estimated intramolecular H-bond energy for malonaldehyde
suggests the value of about 12 kcal/mol. The correlations
between the properties of RCPs and H-bond energy are not
linear but the above-mentioned results indicate that H‚‚‚H
interactions for BDMP and PDMP are not meaningless.
molecular structures have been optimized; styrene, a fluoro
derivative for which X ) F, a derivative with Y ) F, and a
fourth molecular structure with X and Y ) F. The starting
geometries for the styrene derivatives were obtained with the
use of the MOLEKEL program.52 All structures were optimized
as planar systems, for the first three the stable structures were
obtained without imaginary frequencies but for the fourth one
with X, Y ) F there is one imaginary frequency, suggesting
that the system corresponds to the transition state. It is worth
mentioning that the stable configuration was achieved for
styrenesthe modeled system corresponding to BDMP and
PDMP molecules. It strongly supports the idea of the existence
of intramolecular dihydrogen bonds for BDMP and PDMP.
Figure 4 shows the molecular graph and the contour density
electron map of the styrene molecule. The bond critical
point of H‚‚‚H for the intramolecular dihydrogen bond
was found, a situation similar to that observed for BDMP and
PDMP. There is also the ring critical point (RCP) close to the
BCP of H‚‚‚H and existing due to the creation of an intramo-
lecular hydrogen bond (Figure 4). A similar situation is observed
for the other modeled systems with fluoro substituents. BCPs
were found for the X‚‚‚Y interaction, even if both X and Y are
fluoro substituents. And for all cases there are the ring critical
points close to the BCPs of X‚‚‚Y contacts. For two cases of
H‚‚‚F contacts the situation is not surprising; there are intramo-
lecular C-H‚‚‚F hydrogen bonds, namely, -CdCsH‚‚‚F and
C(benzene)sH‚‚‚FsCdC- systems. But there is also the bond
path and BCP for the F‚‚‚F interaction; this kind of interaction
was described earlier in terms of the Bader theory.53 The steric
interactions in ortho-substituted biphenyl were investigated by
Cioslowski and Mixon,53 the authors explained that BCPs are
not necessarily associated with bonding interactions such as
covalent bonds or hydrogen bonds. When the distance between
two atoms is smaller than their contact interatomic separation
(CIS) a bond path with BCP appears for a nonbonding repulsive
interaction. We may expect such F‚‚‚F interaction for the styrene
derivative analyzed here because for that structure the transition
state is observed. Table 3 presents the topological parameters
of X‚‚‚Y interactions for BDMP, PDMP and the modeled
styrene derivative molecules. For all cases the topological criteria
of the existence of hydrogen bonding given by Koch and
Popelier47 are fulfilled.
For the investigated crystal structures there are the following
Mulliken charges for hydrogen atoms: +0.138 and -0.050 au
for BDMP for H(Cd) and HsC(benzene) hydrogen atoms and
the corresponding charges for PDMP amount to 0.144 and
-0.046 au, respectively.
DFT and AIM Calculations for Styrene Derivatives. Chart
1 presents the styrene molecule, which may be treated as a
fragment of BDMP and PDMP molecules containing the
corresponding H‚‚‚H interaction (hydrogen atoms designated
as X and Y).
Figure 5 shows the dependence between the energy of the
system and the torsion angle. The curves were constructed for
all four cases of styrene and its derivatives. The torsion angle
is the one concerning the following fragment of the molecule
(see Chart 1); (Y)CsCsCdC(X). We have obtained the planar
conformation for the torsion angle equal to zero. For that angle
being equal to 90° we have the XHCdCH- substituent
To get a more detailed insight into this kind of interaction,
the B3LYP/6-311++G** calculations have been performed on
the modeled systems; styrene and its fluoro derivatives. Four

1836 J. Phys. Chem. B, Vol. 108, No. 6, 2004
Grabowski et al.
Figure 5. Dependence between the energy of the system and the
torsional angle. Circles correspond to styrene, squares to the derivative
with CdCsF‚‚‚HsC(benzene) H-bond, triangles to the molecule with
CdCsH‚‚‚FsC(benzene) H-bond, and open circles to the difluoro
derivative. Energies are given in kcal/mol and angles in degrees; for
all systems the energies are normalized that the lowest energy
corresponds to zero.
TABLE 4: Geometrical Parameters of C-X‚‚‚Y-C
Contacts (in Ångstroms and Degrees) for Styrene and Its
Derivatives (See Chart 1); Results of B3LYP/6-311++G**
Calculations
C-X‚‚‚Y-C X‚‚‚Y
C-X
C-Y
C-X‚‚‚Y C-Y‚‚‚X
C-H‚‚‚H-C
C-H‚‚‚F-C
C-F‚‚‚H-C
C-F‚‚‚F-C
2.208
2.260
2.282
2.569
1.084 1.084
1.080 1.358
1.355 1.081
1.342 1.349
111.0
115.1
101.3
100.1
115.3
107.2
120.6
110.3
symmetric in the range from 0 to 180° with the maximum at
90°; for two other cases the curves are not symmetric. The main
conclusion is that for three cases for which the stable planar
conformations were found they are of the lowest energies; for
the transition planar state with X, Y ) F we have got the most
stable conformation for the torsion angle equal to 40°. It strongly
supports the idea that for three cases considered here there are
the intramolecular hydrogen bonds, intramolecular dihydrogen
bond CsH‚‚‚HsC, and intramolecular CsH‚‚‚F H-bonds; for
one case there is the steric, nonbonding F‚‚‚F interaction existing
for the planar transition state.
Table 4 shows the geometrical C-X‚‚‚Y-C parameters (see
Chart 1) for styrene and its derivatives calculated at the B3LYP/
6-311++G** level of theory. These results show that the
geometrical criteria again cannot be decisive to define the
character of X‚‚‚Y interactions because H‚‚‚H and H‚‚‚F
distances are only slightly less than the corresponding sums of
van der Waals radii -2.4 and 2.55 Å, respectively. Additionally,
C-H‚‚‚H and C-H‚‚‚F angles are far from linearity.
Figure 4. Molecular graph and the contour density map of styrene.
TABLE 3: Topological Parameters of Intramolecular
Interactions of Styrene Derivatives and of BDMP and PDMP
Moleculesa
2
2
X‚‚‚Y
FX‚‚‚Y
∇ FX‚‚‚Y
FRCP
∇ FRCP
Summary
H‚‚‚H (BDMP)
H‚‚‚H (PDMP)
H‚‚‚H (styrene)
F‚‚‚H (styr.der.)
H‚‚‚F (styr.der)
F‚‚‚F (styr der.)
0.0105
0.0112
0.0089
0.0130
0.0141
0.0149
0.0396
0.0419
0.0363
0.0505
0.0568
0.0639
0.0102
0.0107
0.0089
0.0091
0.0099
0.0074
0.0508
0.0542
0.0403
0.0518
0.0572
0.0434
The crystal structures of [4-((E)-but-1-enyl)-2,6-dimethoxy-
phenyl]pyridine-3-carboxylate (BDMP) and [4-((E)-pent-1-
enyl)-2,6-dimethoxyphenyl]pyridine-3-carboxylate (PDMP) in-
vestigated here show that H‚‚‚H intramolecular contacts exist
that may be treated as intramolecular C-H‚‚‚H-C dihydrogen
bonds. The application of the Bader theory to the geometries
of BDMP and PDMP molecules taken from the crystal structure
measurements shows that the topological criteria of the existence
of hydrogen bonding are fulfilled. The additional calculations
performed at the B3LYP/6-311++G** level of theory for
styrene and its derivatives support the idea of the existence of
C-H‚‚‚H-C intramolecular hydrogen bonds.
a X‚‚‚Y contacts are taken into account and rings created due to
such interactions: -YsC(benzene)sC(benzene)sC(aliphatic)dCsX
rings. All values are given in au; results of B3LYP/6-311++G**
calculations.
perpedicular to the plane of the benzene ring. The range of the
torsion angle of 0-90° is considered here (Figure 5). For two
cases, C6H5sCHdCH2 and C6H5sCHdCFH, the curves are

Crystal and Molecular Structures of BDMP and PDMP
J. Phys. Chem. B, Vol. 108, No. 6, 2004 1837
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