Inter- and intramolecular hydrogen bonds - Structures of 1-methylpyrrole-2-carboxamide and 1-hydroxypyrrole-2-carboxamide

Article abstract of DOI:10.1016/j.molstruc.2007.03.053

The structures of 1-methylpyrrole-2-carboxamide (MPCA) and 1-hydroxypyrrole-2-carboxamide (HPCA) are analyzed, for both structures B3LYP/6-311++G(d,p) calculations were performed on s-cis and s-trans conformations and on monomeric and dimeric forms of these conformers. N-H?O hydrogen bonds exist for dimers. The X-ray crystal structure of MPCA is also analyzed; centrosymmetric dimers of syn conformers connected through N-H?O hydrogen bonds exist in crystal structure as well as C-H?O intramolecular interactions possessing some of characteristics typical for hydrogen bond.

Full text of DOI:10.1016/j.molstruc.2007.03.053

Available online at www.sciencedirect.com
Journal of Molecular Structure 844–845 (2007) 173–180
www.elsevier.com/locate/molstruc
Inter- and intramolecular hydrogen bonds – Structures of
1-methylpyrrole-2-carboxamide and 1-hydroxypyrrole-2-carboxamide
a,
a
b
Sławomir J. Grabowski *, Marcin Palusiak , Alina T. Dubis ,
c
c
Arno Pfitzner , Manfred Zabel
a
Department of Crystallography and Crystal Chemistry, University of Ło´dz´, 90-236 Ło´dz´, ul.Pomorska 149/153, Poland
b
Institute of Chemistry, University of Białystok, Al. J. Piłsudskiego 11/4, 15-443 Białystok, Poland
c
Institut fu¨r Anorganische Chemie der Universita¨t Regensburg, 93040 Regensburg, Germany
Received 23 February 2007; received in revised form 26 March 2007; accepted 26 March 2007
Available online 10 April 2007
This paper is dedicated to Professor Lucjan Sobczyk on the occasion of his 80th birthday
Abstract
The structures of 1-methylpyrrole-2-carboxamide (MPCA) and 1-hydroxypyrrole-2-carboxamide (HPCA) are analyzed, for both
structures B3LYP/6-311++G(d,p) calculations were performed on s-cis and s-trans conformations and on monomeric and dimeric forms
of these conformers. N–Hꢀ ꢀ ꢀO hydrogen bonds exist for dimers. The X-ray crystal structure of MPCA is also analyzed; centrosymmetric
dimers of syn conformers connected through N–Hꢀ ꢀ ꢀO hydrogen bonds exist in crystal structure as well as C–Hꢀ ꢀ ꢀO intramolecular inter-
actions possessing some of characteristics typical for hydrogen bond.
ꢀ 2007 Elsevier B.V. All rights reserved.
Keywords: Hydrogen bonding; AIM theory; Critical points; Carbonyl group; Pyrrole derivatives; Binding energy
1. Introduction
acceptors’’. The latter terms were introduced by Donohue
[8] and briefly speaking they correspond to the most acidic
and basic groups, respectively; since H-bond may be trea-
ted as the Bronsted acid–Bronsted base interaction [9,10].
It is also worth mentioning that hydrogen bonds may
strongly influence on geometries of molecules, mainly on
the terminal groups of atoms participating in these interac-
tions [3,4]. The elongation of the proton donating bond as
an effect of complexation is mostly observed [11] (so-called
blue shifting hydrogen bonds are an exception [12]), but
also the influence on the proton acceptor is detected [11].
In the latter case one can mention the elongation of
C@O carbonyl group [13] as well as the changes of meth-
oxy groups if H-bonds are formed [14].
It is well known that hydrogen bonds are among inter-
actions which are mostly responsible for the arrangement
of molecules in crystals [1–4]. Different H-bonded motifs
are known, they were systemized and classified; the classi-
fication of Etter [5,6] is very well known but also the other
classifications are often applied, as for example that one
with a synthon term as a type of the motif with H-bond
interaction included [7].
Etter also classified the importance of different hydrogen
bonds [5] and she stated that in crystal structures the exis-
tence of intramolecular six-membered ring H-bonds is pre-
ferred and that after the creation of such rings in crystals
the other intermolecular hydrogen bonds are formed,
mostly between ‘‘good proton donors’’ and ‘‘good proton
Numerous studies on the structures for which the men-
tioned above effects are observed were performed very
recently. One can mention investigations on pyrrole deriv-
atives’ structures. Pyrrole 2-carboxylic acid (PCA) [15] pos-
sesses the proton donating and proton accepting COOH
*
Corresponding author. Fax: +48 42 679 04 47.
E-mail address: slagra@uni.lodz.pl (S.J. Grabowski).
0022-2860/$ - see front matter ꢀ 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2007.03.053

174
S.J. Grabowski et al. / Journal of Molecular Structure 844–845 (2007) 173–180
carboxylic group as well as the N–H proton donating
bond. And really, all of them are involved in hydrogen
bond interactions in the crystal structure of PCA where
the centrosymmetric dimers are formed with two equiva-
lent O–Hꢀ ꢀ ꢀO bonds between carboxylic groups as well as
N–Hꢀ ꢀ ꢀO bonds between N–H pyrrole ring and C@O car-
boxyl group, the C–Hꢀ ꢀ ꢀO interactions also exist [16].
Hence, according to the Etter grafs’ designations [5], fol-
lowing H-bond motifs were detected for the crystal struc-
ture of PCA: R22(8) and R22(10). Similarly, for the crystal
structure of pyrrole-2-carboxamide (PyCa) [17] the same
H-bond motifs exist. For both crystal structures mentioned
here (PCA and PyCa) H-bonds attributed to R22(8) motifs
may be classified as intermolecular resonance assisted
hydrogen bonds [18] since the strength of these interactions
is enhanced owing to the p-electron delocalization [19].
Very recently the crystal structure of 1-methylpyrrol-2-yl
trichloromethyl ketone (PTK) was reported [20] for which
only one typical proton accepting carbonyl group exists
and there are not typical proton donors. As an effect of that
only one type of hydrogen bond exists – C–Hꢀ ꢀ ꢀO. One can
see that because of the lack of typical proton donating
bonds the C–H bond of pyrrole ring acts as the proton
donor. Additionally for the latter crystal structure of
PTK the C–Clꢀ ꢀ ꢀO halogen bonds are formed. For these
interactions C–Cl bonds act as Lewis acids [21–23]. One
can see that for all of the mentioned above crystal struc-
tures being the pyrrole derivatives there is the crucial role
of the carbonyl group influencing the arrangement of mol-
ecules in crystals.
methyl 1-methylpyrrole-2-carboxylate was dissolved in
50 ml of concentrated NH4OH. The reaction mixture was
stirred 48 h at room temperature and the product was
extracted twice with ether. The extract was dried over
MgSO4 and solvent was evaporated in vacuo. Crude prod-
uct was purified by crystallization from hexane to give 0.4 g
(0.003 mol) of crystal 1-methylpyrrole-2-carboxamide
(MPCA).
Mp 95 ꢁC (decomposition).
IR (KBr, m cmꢁ1): 3378, 3183, 2951, 1639, 1605, 1529,
ꢀ
1285, 729, 606, 512.
1H NMR (DMSO) d ppm: 6.86 (1H, m, Ar-H); 6.78 (1H,
m, Ar-H); 5.98 (1H, m, Ar-H); 3.82 (3H, s, NCH3).
13C NMR (DMSO) d ppm: 163.2 (C@O); 127.85 (CH);
125.28 (C); 113.06 (CH); 106.53 (CH); 36.25 (CH3).
2.3. X-ray measurements
Colorless, needle crystal of 1-methylpyrrole-2-carbox-
amide (MPCA), mounted on glass fiber, was used for dif-
fraction measurement. The data were collected on a
STOE IPDS imaging plate single crystal diffractometer
[27] with low temperature device, using MoKa source and
a graphite monochromator. Data reduction was performed
with the STOE IPDS-software package [27]. The Lorentz
and polarization corrections were applied. Cell parameters
were determined by indexing of 8000 reflections with I/
r(I) > 6.0.
The structure was solved by direct methods using SIR-
97 [28] and refined by full-matrix least-squares methods
on F2 using SHELXL97 [29]. All nonhydrogen atoms were
refined with anisotropic thermal displacement parameters.
Hydrogen atoms were located geometrically using AFIX
in SHELXL97 [29]. At the final stage of structure refine-
ment H atoms attached to non-carbon atoms (H211 and
H212) were fully refined with isotropic thermal displace-
ments. Molecular geometries were calculated by PARST
[30]. Graphical presentation of molecules was performed
using PLATON [31]. The crystal data and details of the
X-ray analysis are given in Table 1. Table 2 presents the
selected geometrical parameters of MPCA. Fig. 1 shows
the molecular structure of MPCA with the designations
of atoms used in further tables and discussions, Fig. 2
shows the part of the crystal lattice of MPCA where H-
bonds are visible. Crystallographic data for the structural
analysis have been deposited with the Cambridge Crystal-
lographic Data Centre (Deposition No.: CCDC 637873).
The aim of this study is to analyze the crystal structure
of 1-methylpyrrole-2-carboxamide (MPCA) since it
belongs the series of structures mentioned above possessing
the C@O proton acceptor centre. Additionally DFT calcu-
lations for the monomers and dimers of MPCA were
performed as well as for analogous systems of 1-hydroxy-
pyrrole-2-carboxamide (HPCA). The QTAIM (Quantum
Theory of ‘‘Atoms in Molecules’’) [24,25] was applied for
these systems to deepen the characteristics of H-bond
interactions.
2. Experimental
2.1. General methods
Melting point was measured on Buchi B-540 appara-
¨
tus. NMR spectra were recorded with the Bruker AC
200F (200 MHz) spectrometer using DMSO solution with
TMS as an internal standard. Infrared spectra were
recorded on Nicolet Magna-IR 550 Series II as a KBr pel-
lets. All solvents were dried and freshly distilled prior to
use.
2.4. Computational details
The calculations have been carried out using the Gauss-
ian03 set of codes [32]. The B3LYP method is applied; this
method is a hybrid density functional theory approach
which combines Becke’s three-parameter nonlocal exchange
potential with the nonlocal correlation functional of Lee,
Yang and Parr [33]. The inclusion of diffuse components
in the basis set is desired to describe properly the hydrogen
2.2. Synthesis of the 1-methylpyrrole-2-carboxamide
Synthesis of MPCA proceeding according to the
description given by Israel [26]. One gram (0.007 mol)

S.J. Grabowski et al. / Journal of Molecular Structure 844–845 (2007) 173–180
175
Table 1
Crystallographic data and structure refinement
Formula
Mw
C6H8N2O
124.14
Crystal system
Space group
Monoclinic
P21/c
˚
a (A)
9.791(8)
4.858(3)
14.004(13)
107.96(10)
633.6(9)
4
1.301
0.092
173(1)
˚
b (A)
˚
c (A)
b (deg)
3
˚
V (A )
Z
Dx (g cmꢁ3
)
l (mmꢁ1
T (K)
)
˚
k (A)
0.71073
ꢁ11 6 h 6 11
ꢁ5 6 k 6 5
ꢁ17 6 l 6 17
5375
Fig. 1. Drawing of MPCA molecule with atom labeling scheme.
Displacement ellipsoids of non-hydrogen atoms are drawn at the 50%
probability level. Hydrogen atoms are shown as spheres of arbitrary radii.
Index ranges
No. of data collected
No. of unique data
Rint
1199
0.0365
No. of I > 2r(I) data
No. of parameters
R1 (all data)
980
90
0.0493
wR2 (all data)
0.1075
R1 [I > 2r(I)]
0.0402
wR2 [I > 2ꢁr3(I)]
0.1034
˚
Dqmin (eAꢁ3
)
ꢁ0.164
˚
Dqmax (eA
)
0.218
Table 2
Selected geometric parameters for 1-methylpyrrole-2-carboxamide
´
˚
(MPCA) [A, ꢁ]
N1–C2
N1–C5
N1–C11
N21–C21
O21–C21
1.384(2)
1.364(2)
1.459(2)
1.345(2)
1.242(2)
Fig. 2. Network of intermolecular contacts in the crystal structure of
MPCA. N–Hꢀ ꢀ ꢀO interactions are shown with dotted lines. Non-hydrogen
atoms are drawn as spheres of arbitrary radii: black corresponds to
carbon, red – to oxygen, blue – to nitrogen. (For interpretation of the
references to color in this figure legend, the reader is referred to the web
version of this paper.)
C2–C21–O21
C2–C21–N21
N21–C21–O21
C2–N1–C5
122.7(2)
115.4(2)
121.9(2)
108.2(2)
123.3(2)
N1–C2–C21
C4–C5–N1–C11
C3–C2–C21–O21
C3–C2–C21–N21
C2–C3–C4–C5
C3–C4–C5–N1
176.2(2)
152.9(2)
ꢁ25.9(2)
ꢁ0.5(2)
1.0(2)
carbonyl group lies at the same side of N–CH3 of pyrrole
ring and s-trans where these groups are at the opposite
sides of molecule. It is worth to mention that for the crystal
structure of pyrrole-2-carboxylic acid (PCA) [16] analyzed
previously the s-cis conformation exists, the same s-cis
conformer is observed for pyrrole-2-carboxamide crystal
structure [17]. The crystal structure results presented here
for 1-methylpyrrole-2-carboxamide (MPCA) also show
the existence of that conformation.
The B3LYP/6-311++G** calculations on dimers of both
conformers of MPCA were carried out here. These are
centrosymmetric dimers connected through equivalent
N–Hꢀ ꢀ ꢀO hydrogen bonds. Fig. 3 presents the molecular
graphs for both kinds of dimers of MPCA. Since for mono-
meric and dimeric forms of s-cis conformation of MPCA a
weak C–Hꢀ ꢀ ꢀO intramolecular hydrogen bond may exist
bonding interaction thus the 6-311++G** basis set [34]
was applied for calculations since H-bonded systems were
considered here. In other words the B3LYP/6-311++G**
level of theory was applied for all calculations performed
here. The wave functions obtained within this level of
approximation were further applied for the calculations
performed with the use of AIM2000 program [35]. This
program allows to determine topological parameters based
on the Bader theory. Hence critical points (CPs) were local-
ized and their properties such as electron densities at CPs
and their Laplacians were analysed.
In this study two conformations of 1-methylpyrrole-2-
carboxamide are analyzed, s-cis conformer where C@O

176
S.J. Grabowski et al. / Journal of Molecular Structure 844–845 (2007) 173–180
Fig. 4. Molecular graphs of dimers of s-syn and s-trans conformers of
HPCA, big circles designate attractors attributed to the positions of nuclei
while small circles designate critical points, bond paths are also shown.
Fig. 3. Molecular graphs of dimers of s-syn and s-trans conformers of
MPCA, big circles designate attractors attributed to the positions of nuclei
while small circles designate critical points, bond paths are also shown.
tal structures of carboxylic acids as well as of amides. The
geometrical parameters of that N–Hꢀ ꢀ ꢀO hydrogen bond
(N21-H212ꢀ ꢀ ꢀO2100) are given in Table 3, the Nꢀ ꢀ ꢀO dis-
˚
tance is equal to 2.982 A and the system is close to the lin-
thus analogeous calculations were carried out on 1-
hydroxypyrrole-2-carboxamide (HPCA). The latter system
was chosen since in such a case the stronger than C–Hꢀ ꢀ ꢀO
interactions may exist, these are O–Hꢀ ꢀ ꢀO bonds. For
HPCA the analogous calculations as for MPCA were per-
formed here. These are calculations on s-cis and s-trans
conformers, in the former case the OH hydroxyl group is
placed at the same side as C@O group, the calculations
on the corresponding centrosymmetric dimers of HPCA
were also carried out here. Fig. 4 shows the molecular
graphs for both dimers of HPCA.
It is worth mentioning that all systems considered here
correspond to energy minima since no imaginary frequen-
cies were observed. That is observed even for dimers where
symmetry constraints were applied connected with the exis-
tence of the inversion centre between interacting MPCA
and HPCA molecules. The calculations of binding energies
were performed to take into account the deformation of
molecules as a result of complexation [36] as well as to
include the BSSE correction according to Boys and Ber-
nardi [37].
earity since the N–Hꢀ ꢀ ꢀO angle is equal to 168.0ꢁ. The
analogous distance for the PyCa crystal structure is equal
˚
to 2.987 A and the N–Hꢀ ꢀ ꢀO angle amounts to 145.8ꢁ;
for the crystal structure of PCA the O–Hꢀ ꢀ ꢀO H-bonds
˚
exist with Oꢀ ꢀ ꢀO distance of 2.647 A, less than Nꢀ ꢀ ꢀO dis-
tances mentioned above. Additionally, O–Hꢀ ꢀ ꢀO angle
amounts to 176.3ꢁ, this is closer to the linearity than
N–Hꢀ ꢀ ꢀO bridges are. It is well known that generally
homonuclear O–Hꢀ ꢀ ꢀO hydrogen bonds are stronger than
heteronuclear N–Hꢀ ꢀ ꢀO ones, and as a consequence the
former ones have shorter Hꢀ ꢀ ꢀO distances. For example,
this is observed for O–Hꢀ ꢀ ꢀO and N–Hꢀ ꢀ ꢀO hydrogen
bonds of carboxylic acids and amides, respectively. It was
stated that these H-bonds in carboxylic acids and amides
may be classified as intermolecular resonance assisted
hydrogen bonds [18]. The detailed analysis of these interac-
tions was performed [38] and it was found that for carbox-
ylic acids the electrostatic interaction energy term is the
most important attractive one. This is in line with the
postulate of Pauling who stated that H-bonds are mostly
electrostatic interactions [39]. However the other attractive
term, delocalization interaction energy, is more important
for carboxylic acids than for amides [38]. It is worth men-
tioning that delocalization seems to be attributed to stronger,
covalent or partially covalent in nature, hydrogen bonds
[40] and that the ratio of electrostatic to delocalization
energies decreases if the strength of H-bond increases [41].
For the MPCA structure analyzed here the C@O car-
bonyl group takes part in the other N–Hꢀ ꢀ ꢀO interaction
(N21-H211ꢀ ꢀ ꢀO210, Fig. 2 and Table 3) with the Nꢀ ꢀ ꢀO
3. Results and discussion
3.1. Crystal structure
Fig. 2 shows the arrangement of molecules in crystals of
MPCA, there are R22(8) H-bonded motifs with two N–
Hꢀ ꢀ ꢀO hydrogen bonds equivalent owing to the symmetry
constraints. Such motifs are also observed for PCA and
PyCa crystal structures and are very common for the crys-
˚
distance equal to 2.944 A and an angle of 157.0ꢁ (Table

S.J. Grabowski et al. / Journal of Molecular Structure 844–845 (2007) 173–180
177
Table 3
˚
The possible hydrogen bonds (distances in A, angles in degrees)
X–Hꢀ ꢀ ꢀY
X–H
Hꢀ ꢀ ꢀY
2.11(2)
2.11(2)
2.56
Xꢀ ꢀ ꢀY
2.944(3)
2.982(3)
2.959(3)
\X–Hꢀ ꢀ ꢀY
157(2)
168(2)
104.0
Symmetry
N21–H211ꢀ ꢀ ꢀO210
N21–H212ꢀ ꢀ ꢀO2100
C11–H112ꢀ ꢀ ꢀO21a
0.88(2)
0.89(2)
0.98
x, ꢁ1 + y, z
ꢁx, 1 ꢁ y, ꢁz
–
a
Intramolecular contact.
3). The similar extra N–Hꢀ ꢀ ꢀO interactions exist in the crys-
tal structure of PyCa. Hence one may say that in both crys-
tal structures, MPCA and PyCa, the carbonyl group
participates at least in two hydrogen bonds – this is so-
called acceptor bifurcated hydrogen bond according to
the terminology introduced by Desiraju and Steiner [3].
Thus there is an additional R24(8) motif for MPCA and
PyCa crystal structures where subscript designates the
number of the proton donating bonds while superscript
the number of acceptors. One can see that for MPCA there
is an extra intramolecular C–Hꢀ ꢀ ꢀO interaction within the
H112–C11–N1–C2–C21–O21 ring (Fig. 1) designated in
terms of the graphs’ nomenclature as S(6). The parameters
of C–Hꢀ ꢀ ꢀO system are presented in Table 3, this interac-
tion may be hardly classified as hydrogen bond since
C–Hꢀ ꢀ ꢀO angle is far from linearity and Hꢀ ꢀ ꢀO distance
close to the sum of the corresponding van der Waals radii.
crystal structure of MPCA analyzed in the previous section
contains dimers of syn conformer.
Analyzing B3LYP/6-311++G** results, if one compares
the monomeric forms with the corresponding dimeric ones
thus regularly for the latter the C@O bond is longer. The
˚
range of C@O bond length is within 1.221–1.259 A. The
longest C@O bond exists for the dimeric form of syn con-
formation of HPCA, for that system the carbonyl group is
involved in intermolecular N–Hꢀ ꢀ ꢀO interaction as well
as in intramolecular O–Hꢀ ꢀ ꢀO bond, two relatively strong
˚
interactions. The shortest C@O bond length of 1.221 A is
detected for monomer of s-trans conformer of MPCA. In
the latter case carbonyl group is not involved in any type
of interaction which may be classified as hydrogen bond-
ing, C@O bond is at the same side as C–H bond of pyrrole
˚
ring, the (C–)Hꢀ ꢀ ꢀO(@C) distance amounts to 2.765 A, this
means that C–Hꢀ ꢀ ꢀO does not fulfil the geometrical criteria
of the existence of hydrogen bonding. For the s-cis MPCA
˚
monomer the C@O bond length is equal to 1.227 A. The
3.2. The role of C@O group in intra- and intermolecular
interactions
elongation of C@O bond in comparison with s-trans con-
former may be an effect of the existence of the intramolec-
ular C–Hꢀ ꢀ ꢀO interaction. However the geometrical
parameters presented in the previous section for the crystal
structure of MPCA indicate the C–Hꢀ ꢀ ꢀO intramolecular
contact being hardly classified as hydrogen bonding.
Fig. 3 presents molecular graphs of dimers of MPCA,
for syn conformation there is the CH3ꢀ ꢀ ꢀO@C bond path
between the C-atom of methyl group and O-atom of car-
bonyl group. The similar Nꢀ ꢀ ꢀC bond path exists between
NH2 and CH3 groups for s-trans conformer. Analogous
paths are observed for the corresponding monomeric forms
of both conformers. For HPCA species there are stronger
It is well known that H-bond formation influences on
geometrical parameters of interacting molecules. Terminal
groups forming H-bridge are mainly changed, however
hydrogen bond also influences distant geometrical parame-
ters [10]. The key role of carbonyl group in formation of
hydrogen bonds was discussed in the previous section.
Table 4 presents geometrical and topological parameters
of C@O group of systems analyzed here, these systems
were calculated with the use of B3LYP/6-311++G(d,p)
level of approximation. Monomers and dimers of two con-
formations (s-cis and s-trans) of 1-methylpyrrole-2-carbox-
amide (MPCA) and 1-hydroxypyrrole-2-carboxamide
(HPCA) are considered. It is worth mentioning, that the
electron density
at C=O BCP
Table 4
0.41
0.4
˚
The bond lengths (in A) of C@O group as well as the characteristics of the
corresponding BCP (in a.u.); electron density at BCP – qC, its Laplacian –
$2qC, kinetic electron energy density at BCP – GC, potential electron
energy density at BCP – VC
0.39
System
C@O
qC
$2qC
GC
VC
R2 = 0.9958
MPCA-mon. s-syn
MPCA-mon. s-trans
HPCA-mon. s-syn
HPCA-mon. s-trans
MPCA-dim. s-syn
MPCA-dim. s-trans
HPCA-dim. s-syn
HPCA-dim. s-trans
1.227
1.221
1.244
1.222
1.241
1.238
1.259
1.237
0.4015
0.4062
0.3874
0.4064
0.3877
0.3911
0.3728
0.3920
ꢁ0.3558
ꢁ0.3165
ꢁ0.4420
ꢁ0.3381
ꢁ0.4183
ꢁ0.3975
ꢁ0.4799
ꢁ0.4081
0.5823
0.6040
0.5261
0.5992
0.5323
0.5463
0.4807
0.5457
ꢁ1.2536
ꢁ1.2870
ꢁ1.1627
ꢁ1.2830
ꢁ1.1691
ꢁ1.1920
ꢁ1.0814
ꢁ1.1935
0.38
0.37
1.22
1.23
1.24
1.25
1.26
C=O bond length
˚
Fig. 5. The relationship between C@O bond length (in A) and the electron
density at corresponding bond critical point (in a.u.).

178
S.J. Grabowski et al. / Journal of Molecular Structure 844–845 (2007) 173–180
N–Hꢀ ꢀ ꢀO and O–Hꢀ ꢀ ꢀO interactions and the Hꢀ ꢀ ꢀO bond
paths exist in these cases (Fig. 4).
parameters of C–Hꢀ ꢀ ꢀO and C–Hꢀ ꢀ ꢀN interactions do not
directly correspond to Hꢀ ꢀ ꢀO and Hꢀ ꢀ ꢀN contacts since
Cꢀ ꢀ ꢀO and Cꢀ ꢀ ꢀN bond paths exist. The results concerning
Hꢀ ꢀ ꢀO contacts of all monomers and dimers are included in
Table 5. One can see that the intramolecular interactions
are stronger than intermolecular ones since the appropriate
contacts of the former are shorter and the electron densities
of corresponding BCPs are greater. Fig. 7 presents the rela-
tionship between Hꢀ ꢀ ꢀO distance and the electron density
at the corresponding BCP; this is not linear correlation.
The correlation between bond length of C@O and the elec-
tron density at BCP analyzed in the previous section is lin-
ear (Fig. 5); however the range of C@O bond lengths is of
Table 4 shows changes of C@O bond length being in line
with the changes of topological parameters. Fig. 5 presents
the linear relationship between C@O bond length and the
electron density at the corresponding bond critical point
(qC), the greater qC corresponds to the shorter and stronger
C@O bond. The other topological parameters also corre-
late with the C@O bond length (Fig. 6), these are: Lapla-
cian of the electron density at C@O BCP – $2qC, the
total, kinetic and potential electron energy densities at this
BCP (HC, GC and VC, respectively).
˚
about 0.04 A. The range of Hꢀ ꢀ ꢀO contacts presented in
˚
3.3. The Hꢀ ꢀ ꢀO contact
Fig. 7 amounts to 0.49 A, 10 times more. It is well known
that the relationship between the atom-atom distance and
the electron density at corresponding BCP is generally
exponential and it may be approximated as the linear rela-
tion for narrower ranges of distances. In the case of the
relationship presented in Fig. 7 the power function correla-
tion is indicated and the correlation coefficient is high
(R2 = 0.984), the latter value is slightly lower but still close
to unity if exponential relationship is considered.
Table 4 shows lengths and topological characteristics of
Hꢀ ꢀ ꢀO contacts in intramolecular N–Hꢀ ꢀ ꢀO and O–Hꢀ ꢀ ꢀO
H-bonds as well as such contacts of intermolecular N–
Hꢀ ꢀ ꢀO bonds. The parameters of intramolecular C–Hꢀ ꢀ ꢀO
and C–Hꢀ ꢀ ꢀN interactions (Fig. 3) are not presented since
these are weaker interactions which are hardly classified
as hydrogen bonds if they are at all. The topological
AIM
parameter
electron density
at H...O BCP
0.8
GC, R2 = 0.9962
0.06
0.05
0.04
0.03
0.02
0.01
0.4
C=O bond length
0
1.22
-0.4
1.23
1.24
1.25
1.26
Laplacian, R2 = 0.9682
H
C, R2 = 0.995
-0.8
-1.2
-1.6
-3.9969
y= 0.3818x
R2=0.984
VC, R2 = 0.9969
0
1.6
1.7
1.8
1.9
2
2.1
2.2
H...O distance
˚
Fig. 6. The relationship between C@O bond length (in A) and the
characteristics of the corresponding bond critical point such as, Laplacian,
GC, VC and HC (all in a.u.).
˚
Fig. 7. The relationship between Hꢀ ꢀ ꢀO distance (in A) and the electron
density at corresponding bond critical point (in a.u.).
Table 5
2
˚
The Hꢀ ꢀ ꢀO distance (in A) as well as the characteristics of the corresponding BCP (in a.u.); electron density at BCP – qC, its Laplacian – $ qC, kinetic
electron energy density at BCP – GC, potential electron energy density at BCP – VC, for bolded VC and GC values jVCj > jGCj, thus HC < 0
System
H-bond type
Oꢀ ꢀ ꢀH
qC
$2qC
GC
VC
HPCA-mon. s-syn
HPCA-mon. s-trans
MPCA-dim. s-syn
MPCA-dim. s-trans
HPCA-dim. s-syn
O–Hꢀ ꢀ ꢀO intra
N-Hꢀ ꢀ ꢀO intra
N–Hꢀ ꢀ ꢀO inter
N–Hꢀ ꢀ ꢀO inter
N–Hꢀ ꢀ ꢀO inter
O–Hꢀ ꢀ ꢀO intra
N–Hꢀ ꢀ ꢀO inter
N–Hꢀ ꢀ ꢀO intra
1.685
2.163
1.878
1.863
1.879
1.685
1.870
2.149
0.0499
0.0182
0.0295
0.0306
0.0291
0.0499
0.0299
0.0186
0.1378
0.068
0.0411
0.0149
0.0240
0.0249
0.0241
0.0416
0.0244
0.0152
ꢁ0.0477
ꢁ0.0128
ꢁ0.0227
ꢁ0.0239
ꢁ0.0227
ꢁ0.0482
ꢁ0.0231
ꢁ0.0131
0.1011
0.1037
0.1018
0.1401
0.1026
0.0689
HPCA-dim. s-trans

S.J. Grabowski et al. / Journal of Molecular Structure 844–845 (2007) 173–180
179
than intermolecular ones; this is justified not only by the
shorter proton-acceptor distances for intramolecular con-
tacts but also by topological parameters.
AIM parameter
0.15
Laplacian, y = 0.1616x2 - 0.7702x + 0.9781
2 = 0.9994
It is known that for covalent bonds (shared interactions)
[44,45] as well as for very strong hydrogen bonds [46] the
Laplacian of the electron density for interacting pair of
atoms is negative. Such negative Laplacian for H-bonds
indicate their covalent character [46]. However, for strong
hydrogen bonds, if Laplacian is positive but the total elec-
tron energy density at BCP (HC) is negative thus it means
that hydrogen bonding is partially covalent in nature [47].
This is in line with the following equations:
R
0.1
0.05
0
GC, y = 0.1227x2- 0.527x + 0.5811
2 = 0.9997
R
HC, y = -0.0824x2+ 0.3349x - 0.337
H...O distance
R
2 = 0.9994
1.6
1.7
1.8
1.9
2
VC, y = -0.205x2+ 0.8619x - 0.918
2 = 0.9997
2.1
2.2
2.3
2.4
2
1=4r qC ¼ 2GC þ V C
HC ¼ GC þ V C
ð1Þ
ð2Þ
R
-0.05
GC is the positive value while VC is negative, the latter va-
lue is strongly connected with the delocalization energy of
interaction and consequently with covalency. Table 5
shows that HC values Eq. (2) are negative for intramolecu-
lar O–Hꢀ ꢀ ꢀO interactions, for the remaining weaker hydro-
gen bonds HC values are positive.
-0.1
˚
Fig. 8. The relationship between Hꢀ ꢀ ꢀO distance (in A) and the charac-
teristics of the corresponding bond critical point such as, Laplacian, GC,
VC and HC (all in a.u.), different curves were fitted to show relationships.
Fig. 8 presents relationships between Hꢀ ꢀ ꢀO distance
and the other topological parameters. The same relations
concerning C@O bond were linear (see previous section)
while they are non-linear here (see Fig. 8), second order
polynomials were fitted to indicate that generally mono-
tonic non-linear relationships exist between Hꢀ ꢀ ꢀO distance
and any characteristic of the corresponding BCP. The
explanation of such non-linearity is the same as for the cor-
relation between Hꢀ ꢀ ꢀO distance and the electron density at
the corresponding BCP since the broad range of Hꢀ ꢀ ꢀO dis-
tances is considered here.
The intermolecular interactions analyzed here are rela-
tively strong, the binding energies are presented in Table 6
and they are within Æꢁ11.5;ꢁ12.7æ kcal/mol range if the
BSSE correction is included. It is worth to mention that
the binding energies corresponding to s-trans conformers
are greater (modulus of energy), thus interactions for these
conformers are stronger. However s-cis conformers’ dimers
are of the lower energies than their s-trans counterparts.
This is connected with the Leffler–Hammond postulate
[42,43] that systems of stronger H-bonds are closer to tran-
sition states and hence they are of greater energies. It is
worth mentioning that the binding energies of dimers ana-
lyzed here concern two symmetry equivalent N–Hꢀ ꢀ ꢀO
interactions. The intramolecular interactions are stronger
4. Summary
The calculations performed on the monomer and dimer
structures of 1-methylpyrrole-2-carboxamide (MPCA) and
1-hydroxypyrrole-2-carboxamide (HPCA) show the exis-
tence of inter- and intramolecular interactions which may
be classified as hydrogen bonds. For the proton accepting
C@O carbonyl bond its length correlates with topological
parameters of the corresponding bond critical point. The
similar correlations are observed for Hꢀ ꢀ ꢀO contact.
It was found that intramolecular O–Hꢀ ꢀ ꢀO hydrogen
bonds are the strongest ones and they occur in monomer
and dimer of HPCA. The HC values of BCPs of corre-
sponding Hꢀ ꢀ ꢀO interactions are negative indicating the
partial covalency of these hydrogen bonds. The other inter-
esting finding is that intra- and intermolecular hydrogen
bonds of the systems analyzed here do not influence on
each other. The binding energy is more influenced by the
kind of conformer than by the type of compound (MPCA
or HPCA), one can see this from Table 6.
Acknowledgements
Support has been provided by Grant No. 505/706 2006
´ ´
(University of Łodz). Calculations have been carried out in
Table 6
Warsaw (ICM) Supercomputer Center.
The binding energies (in kcal/mol) of dimers analyzed here, the energies
with the BSSE corrections are also presented, the energies of systems in
hartrees
References
System
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energy
Binding energy
(BSSE included)
Energy of the
system
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