Activation of carbon dioxide by bicyclic amidines

Article abstract of DOI:10.1021/jo049243q

Activation of the carbon dioxide molecule was achieved using bicyclic amidines (DBU, PMDBD, and DBN). The solution reaction of CO₂ with amidines yielded the corresponding zwitterionic complexes through the formation of a N-CO₂ bond. ¹³C NMR data confirmed the carbamic nature of the carbamic zwitterions, DBU-CO₂ and PMDBD-CO₂. However, when these adducts were crystallized, the X-ray analyses of the single crystals were in agreement with bisamidinium bicarbonate salt structures, indicating that structural changes occurred in the crystallization process. The elemental and thermogravimetric analysis data for the carbamic zwitterions, DBU-CO₂ and PMDBD-CO₂, initially obtained by the direct reaction of amidines with CO₂, suggest that these molecules are probably associated with one molecule of water by hydrogen-bond formation (amidinium⁺-COO^-...H₂O). A correlation was observed between the thermal stability and the transcarboxylating activity for the amidine-CO₂ complexes. Theoretical calculations of hardness were performed at the B3LYP/cc-pVTZ level of theory and showed concordance with the experimental reactivity of DBU and PMDBD toward CO₂.

Full text of DOI:10.1021/jo049243q

Activation of Carbon Dioxide by Bicyclic Amidines
,
†
†
†
†
Eduardo R. P e´ rez,* Regina H. A. Santos, Maria T. P. Gambardella, Luiz G. M. de Macedo,
†
‡
,†
Ubirajara P. Rodrigues-Filho, Jean-Claude Launay, and Douglas W. Franco*
Instituto de Qu ı´ mica de S a˜ o Carlos, Universidade de S a˜ o Paulo, C. P. 780,
CEP 13560-970, S a˜ o Carlos-SP, Brasil, and Institut de Chimie de la Mati e` re Condens e´ e de Bordeaux,
CNRS UPR 9048, F-33608 Pessac, France
ed5bras@mailcity.com; douglas@iqsc.sc.usp.br
Received May 4, 2004
Activation of the carbon dioxide molecule was achieved using bicyclic amidines (DBU, PMDBD,
and DBN). The solution reaction of CO with amidines yielded the corresponding zwitterionic
complexes through the formation of a N-CO
bond. 13C NMR data confirmed the carbamic nature
of the carbamic zwitterions, DBU-CO and PMDBD-CO . However, when these adducts were
2
2
2
2
crystallized, the X-ray analyses of the single crystals were in agreement with bisamidinium
bicarbonate salt structures, indicating that structural changes occurred in the crystallization process.
The elemental and thermogravimetric analysis data for the carbamic zwitterions, DBU-CO
PMDBD-CO , initially obtained by the direct reaction of amidines with CO , suggest that these
molecules are probably associated with one molecule of water by hydrogen-bond formation
2
and
2
2
+
-
(
amidinium -COO ‚‚‚H
transcarboxylating activity for the amidine-CO
were performed at the B3LYP/cc-pVTZ level of theory and showed concordance with the
experimental reactivity of DBU and PMDBD toward CO
2
O). A correlation was observed between the thermal stability and the
2
complexes. Theoretical calculations of hardness
2
.
Introduction
catalytic activity of these bases is, in many cases,
associated with their proton-transfer activity.
We have reported, for the first time, the fixation and
subsequent transfer of carbon dioxide by 1,8-diazabicyclo-
Carbon dioxide is considered to be a weak Lewis acid,1
and a preliminary activation of the CO
commonly required to insert it into organic molecules.
The activation of carbon dioxide has been performed by
2
2
molecule is
[
5.4.0]undec-7-ene (DBU) in the synthesis of N-alkyl-
7
carbamates. Other authors have also reported nucleo-
philic catalysis by cyclic amidines and guanidines in
diverse carbon dioxide reactions through the formation
3
electrochemical reduction in both aqueous and nonaque-
4
ous media. Inorganic and organometallic compounds
5
have also been used for this effect. Hindered amidine
adduct.8
2
of an intermediate base-CO
and guanidine bases have been used as catalysts in
DBU9 and 3,3,6,9,9-pentamethyl-2,10-diazabicyclo-
reactions involving the use of carbon dioxide.2
a,c-e,6
The
10
[4.4.0]dec-1-ene (PMDBD) in acid-base reactions, with
*
Authors to whom correspondence should be addressed. Phone/
(5) (a) Nomura, R.; Hasegawa, Y.; Ishimoto, M.; Toyosaki, T.;
Fax: +55-16-33-73-9976 (D.W.F.).
Matsuda, H. J. Org. Chem. 1992, 57, 7339. (b) Sakakura, T.; Choi, J.;
Matsuda, T.; Sako, T.; Oriyama, T. J. Org. Chem. 1999, 64, 4506. (c)
Chu, F. X.; Dueno, E. E.; Jung, K. W. Tetrahedron Lett. 1999, 40, 1847.
(d) Kim, S. I.; Chu, F. X.; Dueno, E. E.; Jung, K. W. J. Org. Chem.
1999, 64, 4578. (e) Yin, X.; Moss, J. R. Coord. Chem. Rev. 1999, 181,
27 and references therein. (f) Sievers, M. R.; Armentrout, P. B. Inorg.
Chem. 1999, 38, 397. (g) Konno, H.; Kobayashi, A.; Sakamoto, K.;
Fagalde, F.; Katz, N. E.; Saitoh, H.; Ishitani, O. Inorg. Chim. Acta 2000,
299, 155. (h) Field, L. D.; Lawrenz, E. T.; Shaw, W. J.; Turner, P. Inorg.
Chem. 2000, 39, 5632. (i) Tai, C. C.; Pitts, J.; Linehan, J. C.; Main, A.
D.; Munshi, P.; Jessop, P. G. Inorg. Chem. 2002, 41, 1606. (j) Pushkar,
J.; Wendt, O. F. Inorg. Chim. Acta 2004, 357, 1295.
†
Universidade de S a˜ o Paulo.
CNRS UPR 9048.
‡
(
1) Aresta, M.; Forti, G. Carbon Dioxide as a Source of Carbon:
Biochemical and Chemical Uses; NATO ASI Series; D. Reidel Publish-
ing Co.: Dordrecht, The Netherlands, 1987.
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E. Chem. Lett. 1974, 427. (b) Behr, A. Carbon Dioxide Activated by
Metal Complexes; VCH: Weinheim, Germany, 1988. (c) Waldman, T.
E.; McGhee, W. J. Chem. Soc., Chem. Commun. 1994, 957. (d) McGhee,
W.; Pan, Y.; Riley, D. P. J. Chem. Soc., Chem. Commun. 1994, 699. (e)
McGhee, W.; Riley, D. J. Org. Chem. 1995, 60, 6205. (f) Kim, S. I.;
Chu, F. X.; Dueno, E. E.; Jung, K. W. J. Org. Chem. 1999, 64, 4578.
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2000, 41, 1051.
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1
0.1021/jo049243q CCC: $27.50 © 2004 American Chemical Society
Published on Web 10/09/2004
J. Org. Chem. 2004, 69, 8005-8011
8005

P e´ rez et al.
SCHEME 1
the formation of adducts involving the corresponding
amidinium cation, are examples of the behavior of
CO
2
(DBU-CO
2
zwitterion) suggest that the complex
could be associated with water, probably by a hydrogen-
bond interaction with the CO moiety. The carbamic
DBU-CO complex was crystallized from a 4:1 (v/v)
ethanol/ether solution, and single crystals were collected
for X-ray studies. The X-ray revealed that the crystals
correspond to a bis[DBUH] HCO
that the structural changes that occur in the crystalliza-
tion process transformed the starting carbamic zwitterion
amidines as bases, as expected according to their pK
a
1
2
1
(conjugate acid pK) values, which are greater than 23.
2
On the other hand, there are some examples of the use
12
of DBU as a nucleophilic base. DBU has also been used
as a nucleophile in its reaction with phosphorochloridates
to form DBU-phosphorus intermediates via N-P bond
+
-
3
structure, suggesting
1
3
formation. Another study has shown the effect of DBU
as a Lewis base in the Baylis-Hillman reaction, leading
to abnormal adducts containing the amidine moiety.14
The present paper describes a comparative study of the
reactivities of a number of cyclic amidines toward the
carbon dioxide molecule. Two novel complexes have been
obtained from the reaction of DBN and PMDBD amidines
+
-
into a bicarbonate salt. The data for bis[DBUH] HCO
3
were corrected by absorption factors using the PSISCAN
method.15 The structure was solved by the SIR92 method
16
17
and refined by the full-matrix least-squares and differ-
1
8
ence Fourier syntheses, using the WingX system. The
hydrogen atoms (except those attached to the N and O
atoms that are found in the DF map) were located in their
ideal positions, with a thermal vibration equal to 1.2
times the Ueq of the attached atom, and not refined. All
non-hydrogen atoms were refined anisotropically.
The asymmetric unit of [DBUH] HCO3 with the atom-
numbering scheme is depicted in Figure 1a. The molec-
ular structure consists of dimeric species, as shown in
Figure 1b.
The dimer exhibits a strong hydrogen bond (N1‚‚‚O2
) 2.693(2) Å) between the N-H of the protonated DBU
molecule and one of the oxygen atoms of the bicarbonate
anion. The dimer arises from very strong hydrogen bonds,
which are formed between the HCO
2
with CO in solution. X-ray structures have been deter-
mined for the DBU and PMDBD bicarbonates. The
transcarboxylating activity, an important reaction for
both combinatorial syntheses and simulation of enzy-
matic systems, is correlated with the thermal stability
of the amidine-CO complexes.
2
Theoretical calculations have also been carried out to
obtain the relative hardness for both DBU and PMDBD
+
-
molecules and their respective adducts with CO
2
. This
study provides a better understanding of the selective
basic or nucleophilic behavior of the investigated amidines
from the point of view of the HSAB principle.
-
3
ions (O3‚‚‚O1* )
Results and Discussion
2.609(2) Å), across the crystallographic inversion center.
The hydrogen-bond parameters are given in Table 1.
+
Crystal Structure Determination of the [DBUH] -
During the crystallization process of the DBU-CO
2
-
HCO
3
Obtained on Crystallization of the Zwit-
zwitterionic carbamic complex, an amidinium bicarbon-
ate may be formed by the proton transfer from a water
molecule to the zwitterion followed by the nucleophilic
attack of the hydroxyl anion on the N-COOH moiety.
Therefore, an equilibrium involving a carbamic zwitterion
terionic Carbamic DBU-CO
CO zwitterion, represented by structure I in Scheme 1,
was synthesized following the reported procedure. The
2
Complex. The DBU-
2
7
1
3
2
C NMR data for the DBU-CO adduct showed two
signals at 160.7 and 166.4 ppm corresponding to a
carbamic and an amidinium carbon, respectively, con-
firming that it was obtained as a carbamic complex. The
elemental and thermogravimetric (TGA) analyses per-
formed on the solid produced in the reaction of DBU with
is possible, probably in the forms of (DBU-CO
2
)‚H
2
O (I)
(II). This
+
-
and amidinium bicarbonate [DBUH] HCO
3
explanation is summarized in Scheme 1.
Reaction of PMDBD with Carbon Dioxide. Crys-
+
-
tal-Structure Determination of [PMDBDH] HCO
3
.
Scheme 2 shows the formation of a PMDBD-CO zwit-
2
(
10) Denmark, S. E. J. Org. Chem. 1981, 46, 3144.
(
11) Gais, H.-J.; Vollhardt, J.; Kr u¨ ger, C. Angew. Chem. 1988, 100,
1
2
1
2
08.
(
(15) North, A. C. T.; Phillips, D. C.; Mathews, F. S. Acta Crystallogr.
1968, A24, 351.
12) (a) Shieh, W. C.; Dell, S.; Repic, O. J. Org. Chem. 2002, 67,
188. (b) Ghosh, N. Synlett 2004, 574.
(16) Altomare, A.; Cascarano, G.; Giacovazzo, C.; Guagliardi, A. J.
Appl. Crystallogr. 1993, 26, 343.
(
13) Ker s´ , A.; Kers, I.; Stawinski, J. J. Chem. Soc., Perkin Trans. 2
999, 2071.
14) Shi, M.; Xu, Y. M.; Zhao, G. L.; Wu, X. F. Eur. J. Org. Chem.
002, 3666.
(17) Sheldrick, G. M. Instit u¨ t f u¨ r Anorganische Chemie der Uni-
versit a¨ t: G o¨ ttingen, Germany, 1998.
(
(18) Farrugia, L. J. J. Appl. Crystallogr. 1999, 32, 837.
8006 J. Org. Chem., Vol. 69, No. 23, 2004

2
Activation of CO by Bicyclic Amidines
1
9
+
-
FIGURE 1. (a) ORTEP representation of the asymmetric unit of [DBUH] HCO
3
with the atom-labeling system. (b) Dimer
+
-
bis[DBUH] HCO
3
.
TABLE 1. Hydrogen-Bond Parameters for the Dimer,
+
-
Bis[DBUH] HCO3
A-H H‚‚‚B
(Å) (Å)
A‚‚‚B
(Å)
angle
(deg)
A-H‚‚‚B
symmetry
N1-H17‚‚‚O2
0.890 1.800 2.693(2)
173
167
O3-H19‚‚‚O1* 0.860 1.760 2.609(2)
-x, -y, 2 - z
SCHEME 2
FIGURE 2. ORTEP representation of the X-ray structure for
+
-
bis[PMDBDH] HCO
3
.
terionic complex. The yield of the isolated PMDBD-CO
complex was higher than that of the DBU-CO complex
74%) under the same conditions (no water association
was considered). On the other hand, the PMDBD-CO
adduct is soluble in more weakly polar solvents, such as
chloroform and dichloromethane, and seems to be more
2
+
-. The formation of the bicarbonate
bis[PMDBDH] HCO
3
2
is reversible since its dissolution in dry deuterated
chloroform regenerated the zwitterionic species, as con-
firmed by 13C NMR analyses.
(
2
+
-
For the bis[PMDBDH] HCO
3
complex, the X-ray data
collection was conducted at a low temperature (200 K)
since a disordered chloroform molecule was observed in
previous analyses. However, even at low temperatures,
the disorder persists. Figure 2 shows an ORTEP repre-
sentation of the molecule with the atoms identified. For
clarity, the disordered chloroform molecule has been
omitted.
The structure of the complex involved the presence of
hydrogen bonds between the nitrogen and oxygen atoms
of the carbonate. These connections are represented in
Figure 2. The distances of N1‚‚‚O3 and N2‚‚‚O1 are
2.754(3) and 2.744(3) Å, respectively, indicating the
presence of hydrogen bonds of medium strength. The
2
resistant to hydrolysis than the analogous DBU-CO .
The C NMR analysis of the PMDBD-CO carbamic
2
complex (without prior crystallization) in deuterated
chloroform showed three nonequivalent methyl systems
at 24.6, 29.7, and 31.3 ppm. On the other hand, four
methylene signals at 31.4, 31.9, 34.7, and 53.3 ppm were
1
3
detected, revealing the asymmetry of the PMDBD-CO
2
molecule. This suggests that there is some coincidence
in shifts for the two other nonequivalent methyl groups.
1
3
Quaternary carbons were not detected in the C NMR
spectrum. The assignments were confirmed by DEPT-
35° experiments. The 1 C NMR spectrum also showed
3
1
two low-intensity signals at 162.2 and 166.0 ppm (the
signal at 162.2 ppm was weaker) assigned to a carbamate
dimer is formed by the H bonding of two hydrogen
-
bonds between the O2 and O1 atoms of the HCO
3
ions
(
-N-COO) and an amidine (-NdC-N-) carbon, re-
(
O2‚‚‚O1* ) 2.609(3) Å). Table 2 lists the corresponding
spectively. These signals were attributed using reported
NMR data for other amidine derivatives.8
g,20
hydrogen-bond parameters.
Reactivity of 1,5-Diazabicyclo[4.3.0]non-5-ene
As that in the case of the DBU-CO
2
complex, the X-ray
, after its crys-
(
DBN) toward Carbon Dioxide. The reactivity of DBN
structure of the analogous PMDBD-CO
2
2
toward CO was also studied for comparison. DBN
tallization from chloroform, is also consistent with the
formation of a bicarbonate adduct in the form of
amidine is structurally related to DBU; therefore, a
similar behavior was expected in its reaction with CO
and in the transcarboxylation of amines. Scheme 2 shows
the reaction of DBN with CO
2
(
19) Farrugia, L. J. J. Appl. Crystallogr. 1997, 30, 565.
20) Dabak, K. Turk. J. Chem. 2002, 26, 547.
(
2
.
J. Org. Chem, Vol. 69, No. 23, 2004 8007

P e´ rez et al.
TABLE 2. Hydrogen-Bond Parameters for the Dimer,
lated values were 22.4 and 17.4%, respectively), suggest-
ing that these zwitterions were probably associated with
one molecule of water by a hydrogen-bond interaction.
+
-
Bis[PMDBDH] HCO3
A-H
H‚‚‚B
A‚‚‚B
angle
(deg)
A-H‚‚‚B
(Å)
(Å)
(Å)
symmetry
- x,
2
In the case of the DBN-CO adduct, the first weight loss
O2-H1O2‚‚‚O1 1.150(4) 1.490(4) 2.609(3) 162(3) 1/
2
value was more in accordance with the release of a CO
molecule only.
2
3
2
/ - y, -z
N1-H1N‚‚‚O3 0.980
N2-H2N‚‚‚O1 0.950
1.770
1.790
2.754(3)
2.744(3)
178
176
A comparison among the starting temperatures (in
parentheses) for the first weight loss associated with the
amidine-CO
following order of thermal stability for the investigated
complexes: PMDBD-CO (80 °C) > DBU-CO (58 °C)
DBN-CO (30 °C).
On the other hand, from the transcarboxylation experi-
2
breakup allowed the determination of the
SCHEME 3
2
2
>
2
ments using N-cyclohexylamine (yields of carbamates in
parentheses), it was possible to define an order of
reactivity, which correlates inversely to thermal stability
as follows: DBN-CO
2
(68%) > DBU-CO (57%) .
2
TABLE 3. Comparative TGA Results of the DBU-CO2,
PMDBD-CO2, and DBN-CO2 Complexes
PMDBD-CO (negligible).
2
The theoretical calculations discussed below predict the
occurrence of hydrogen-bond interactions between the
first weight
loss T (°C);
mg, %
second weight
loss T (°C);
mg, %
sample
weight (mg)
+
compound
CO
PMDBD-CO
weaker), H20 and H25, respectively (Figure 3). This could
2
oxygen and both a quaternary N -H bond in
2
(stronger) and a C-H bond in DBU-CO
2
DBU-CO2
5.4180
5.1629
5.4660
58-107;
.5549, 28.70
107-170;
(
1
3.8631, 68.29
be a reasonable explanation for both the higher thermal
stability and the lower transcarboxylating activity of the
PMDBD-CO complex.
2
Hardness Calculations. In a N-electron system, with
energy E and external potential v( br , the hardness (η) is
defined using the density functional theory (DFT), as
shown in eq 1.
PMDBD-CO2
DBN-CO2
80-104;
104-150;
3.9650, 76.81
1.2040, 23.32
30-75;
75-94;
0.7034, 12.87
1.5113, 27.65
2
1
As shown in Scheme 3, the formation of the DBN-
CO complex required special conditions. Thus, a solvent
2
2
mixture containing 10% (v/v) of a nonpolar solvent was
used to ensure a high concentration of carbon dioxide in
the reaction medium, and the temperature was decreased
to -10 °C to induce the precipitation of the complex as
it formed. This complex was carefully filtered off from
the solvent and washed with cold ether. It was found to
1 ∂ E
η )
(1)
(2)
(
2
)
2
∂N
v(F/r)
A finite difference approximation of eq 1 gives
I - A
2
η )
2
be more hygroscopic than the DBU-CO homologue and,
therefore, had to be stored under dry and freezing
conditions.
Thermal Stability and Transcarboxylating Activ-
2
ity of the Amidine-CO Carbamic Complexes. The
complexes were studied by TGA to determine their
thermal stability (Table 3). The first weight loss was
where I and A are the ionization potential and the
electron affinity, respectively.
Koopman’s theorem22 can be applied to approximate
eq 2
ELUMO - EHOMO
considered to correspond to CO
the transcarboxylation of the cyclohexylamine with the
amidine-CO zwitterionic complexes were used to cor-
2
release. The results from
η )
(3)
2
2
where ELUMO and EHOMO are the energies associated with
the lowest unoccupied and highest occupied molecular
orbitals, respectively.
relate thermal stability with transcarboxylating activity.
Thus, for the purpose of comparison, the transcarboxy-
lation of cyclohexylamine,7 as a model amine, was
Figure 3 shows the DBU-CO
2
and PMDBD-CO
2
performed at -5 °C with both DBU-CO
2
2
and DBN-CO ,
labeling scheme. Table 4 shows the eigenvalues of
frontier orbitals, HOMO and LUMO, the gap between
them (in atomic units), and the hardness values (in
electronvolts) calculated at the B3LYP/cc-pVTZ level of
theory.
and the corresponding ethyl carbamates were obtained
by a subsequent reaction of the carbamate intermediates
with ethyl iodide for 6 h at 10 °C. Under these conditions,
the yields of the isolated carbamates were 57 and 68%
from the transcarboxylation with DBU-CO
2
and DBN-
First, it is interesting to compare the stability of carbon
dioxide (CO ) and ethanol with DBU and PMDBD.
2
According to our hardness values, the Lewis bases DBU
and PMDBD are on the borderline of the soft-hard scale
CO , respectively. No reaction was detected when the
2
PMDBD-CO complex was used in the range from -5
2
to 80 °C.
The experimental values of the first weight loss for the
DBU-CO and PMDBD-CO carbamic complexes are
more in agreement with the loss of CO and a water
(
they have hardness values of 3.06 and 3.23 eV, respec-
2
2
tively, and PMDBD is a harder base), and both can react
2
molecule (calculated values were 28.9 and 22.9%, respec-
tively) than with the loss of only carbon dioxide (calcu-
(
21) Parr, R. G.; Pearson, R. G. J. Am. Chem. Soc. 1983, 105, 7512.
(22) Pearson, R. G. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 8440.
8008 J. Org. Chem., Vol. 69, No. 23, 2004

2
Activation of CO by Bicyclic Amidines
2 2
FIGURE 3. DFT/B3LYP optimized geometries for DBU-CO (left) and PMDBD-CO (right) with atom labeling.
TABLE 4. B3LYP/cc-pvtz Frontier Orbital Eigenvalues
and Hardness Values
close as possible to a classical Lewis structure for a given
molecule.
EHOMO
ELUMO
gap
(au)
hardness
(eV)
In addition to orbital analysis, it is possible to obtain
further information about the C-N bond character by
comparing the NBO charges of the relevant atoms (Table
molecule
DBU
DBU-CO2
CO2
PMDBD
(au)
(au)
-0.21337
0.01145 -0.22482
3.06
3.03
2.79
3.23
3.06
4.26
-0.25407 -0.03135 -0.22272
-0.34430 -0.13945 -0.20485
5
N
). N13 in PMDBD-CO
in DBU-CO
The charges on C40 (PMDBD-CO
have the same tendency, suggesting that the N-CO
2
is slightly more negative than
4
2
(-0.53125 and -0.50408, respectively).
-0.22076
0.01667 -0.23743
2
) and C28 (DBU-CO
2
)
PMDBD-CO2 -0.25913 -0.03418 -0.22495
ethanol
-0.27422
0.03919 -0.31341
2
bond in PMDBD-CO
polarized) than the corresponding one in DBU-CO
2
is comparatively harder (more
2
.
with the Lewis acid CO
molecule for the purpose of comparison), which is a
harder acid than CO , should only react with PMDBD
2
. Ethanol (calculated as a model
The population analysis clearly shows that the nucleo-
phile center is strongly concentrated on PMDBD’s N13
and DBU’s N and N . From the two electrons that
6 4
populate the HOMO (this population analysis is based
on the 6-311+g* basis set), 1.90418 are on N13 (lone pair),
with 27.92% of s and 72.03% of p character (in PMDBD),
2
due to the high hardness of the PMDBD compared to that
of DBU. This behavior can also be inferred from the
charge values summarized in Table 5.
Table 5 shows the NBO atomic charges for all of the
species. The NBO scheme was adopted for one good
reason; that is, NBO is an approach that comes quite
close to intuitive chemical concepts.
In an initial step, orbitals were associated almost
entirely with a single atom (i.e., core orbitals and lone
pairs are localized just as the so-called natural atomic
orbitals (NAOs)). Next, the orbitals involving bonding (or
antibonding) between pairs of atoms were localized using
only the basis set AOs of those atoms. Finally, the
remaining Rydberg-like orbitals were identified, and all
orbitals were made orthogonal to one another. The result
is that all NAOs and Rydberg orbitals are described using
the basis set AOs of a single atom, and all NBOs are
described using the basis set AOs of two atoms. Thus,
the NBO analysis provided an orbital picture that is as
and 1.72022 on N
character (in DBU). Interestingly, the HOMO-1 of DBU
has 1.91240 on N , the site where the reaction with CO
6
, with 3.21% of s and 96.78% of p
4
2
occurs, with 30.46% of s and 69.48% of p character,
2
clearly showing a mixture (hybridization) of the sp form
(N13 in PMDBD also shows this behavior). This hybrid-
ization favors the formation of the N-CO
HOMO-1 orbital of DBU can overlap easily with the p
orbital of CO (the LUMO orbital of CO is 100% p ), due
to a more favorable geometry, in contrast to the p lone
pair of N (the main contribution of the HOMO orbital
in DBU). As a consequence, a HOMO-1 (DBU) to LUMO
CO ) overlapping occurs when the reaction takes place.
The Wiberg bond indexes (WBI) relative to CO and
2
bond since the
z
2
2
z
y
6
(
2
2
some atoms of DBU and PMDBD provide additional
information about the extra PMDBD-CO stability. A
2
J. Org. Chem, Vol. 69, No. 23, 2004 8009

P e´ rez et al.
TABLE 5. Natural Charges on Relevant Atoms
molecules
molecules
PMDBD-CO2
atom
no.
DBU
DBU-CO2
atom
no.
PMDBD
C
N
C
N
C
H
H
H
C
O
O
3
4
-0.20042
-0.62629
0.48135
-0.53488
-0.42680
0.20839
-0.17134
-0.50408
0.58997
N
C
C
C
N
H
C
O
O
4
5
-0.67439
0.49901
-0.13496
0.08860
-0.60067
0.39369
-0.58717
0.59998
-0.11863
0.14602
-0.53125
0.43416
0.93327
5
6
6
-0.44371
-0.43819
0.24001
12
13
20
40
41
42
11
25
26
27
28
29
30
0.22463
0.21197
0.24316
0.20993
-0.72774
-0.77949
0.91933
-0.75563
-0.76164
hydrogen bond occurs between O42 and H20 (Wiberg bond
index value of 0.0575, greater than the value of 0.0012
drolysis occurs leading to the formation of the respective
+
-
+
-
bis[DBUH] HCO
3
and bis[PMDBDH] HCO
3
salts.
between O29 and H25 in DBU-CO
consisting of O42, C40, N13, C , N , and H20. This hydrogen
bond influences the rotation along the C-N axis between
the planes CO vis- a` -vis PMDBD. The rotation in DBU-
CO is 50° (the dihedral angle C -N -C28-O29), which
2
), forming a ring
There are inverse correlations between the thermal
stability and the transcarboxylating activity for the
5
4
investigated amidine-CO
From the theoretical calculations, the reaction of DBU
with CO occurs under orbitalic control involving the
HOMO-1 orbital of DBU, which can give higher overlap-
ping with the LUMO of the CO molecule. In addition,
2
complexes.
2
2
5
4
2
is much steeper than the angle of 29° in PMDBD. If one
takes into account that H20 is deflected by 9° when the
reaction occurs, the O42-H20 distance (this distance in
the optimized geometry is 1.710 Å) becomes shorter. For
2
the application of the HSAB principle is useful for
understanding the higher reactivity of PMDBD (com-
pared with that of DBU) in proton-transfer reactions with
alcohols and the high reactivity of the two amidines
toward the carbon dioxide molecule.
On the other hand, conformational data show the
existence of strong hydrogen-bond interactions stabilizing
instance, the interaction between CO
-C28) is also weaker in DBU-CO , whose WBI value
is 0.7697, compared to 0.7883 in PMDBD-CO
Another important consequence of bonding CO
2
and nitrogen
(N
4
2
2
.
2
with
PMDBD and DBU is the delocalization of the double
bonds between nitrogen and a neighboring carbon, namely,
2
the PMDBD-CO complex. This, among other factors,
N
N
4
-C
5
-N
double bond (WBI value of 1.6828) is now a
-C -N (Wiberg
bond index values of 1.3692 and 1.3362 between N -C
and C -N in DBU-CO , respectively). The N -C and
-N bond lengths have also changed from their initial
values in DBU to the corresponding ones in DBU-CO
6
(DBU) and N13-C
5
-N
4
(PMDBD). The
can rationalize the selective reaction of PMDBD with
carbon dioxide in the presence of a stronger nucleophile,
such as N-cyclohexylamine.
4
dC
5
resonance bond, for example, part of N
4
5
6
4
5
Finally, the amidines investigated are able to activate
and transfer (DBU and DBN) the carbon dioxide molecule
5
6
2
4
5
C
5
6
to amines. The amidine-CO complexes show an enzyme-
2
2
.
like behavior. Hence, we suggest the use of the investi-
Thus, the N
Å, and the C
4
-C
5
bond length changed from 1.290 to 1.330
gated cyclic amidines and their analogues as model
compounds for biological studies involving carbon dioxide.
5 6
-N bond length changed from 1.380 to
1
C
.340 Å. The same phenomenon occurs among the N13-
5
4 5
-N atoms. The N13dC double bond in PMDBD, which
Experimental Section
has a Wiberg bond index value of 1.7374, becomes a
resonance bond with a WBI of 1.3408 (the bond length
N-Cyclohexylamine, 1,5-diazabicyclo[4.3.0]non-5-ene (DBN),
,8-diazabicyclo[5.4.0]undec-7-ene (DBU), and 3,3,6,9,9-pen-
1
changed from 1.280 to 1.340 Å), and the C
once a single bond with a Wiberg bond index value of
.1278, now has a double bond character with a WBI
value of 1.4049, with the C -N bond length shifting from
.390 Å in PMDBD to 1.320 Å in PMDBD-CO
5
-N
4
bond,
tamethyl-2,10-diazabicyclo[4.4.0]dec-1-ene (PMDBD) were pur-
chased from commercial sources and used without further
purification. The other reagents and solvents were also com-
mercial and had the required purity.
1
5
4
1
2
.
The data collections for X-ray analyses were performed in
+
-
a Cad4 Enraf Nonius diffractometer for bis[DBUH] HCO
3
at
room temperature and in a Kappa CCD at 200 K for
bis[PMDBDH] HCO . The structures were solved using the
3
WinGX system, and the structural analyses were performed
by PLATON.
For the estimation of the hardness of all of the molecules
2 2 2
DBU, DBU-CO , PMDBD, PMDBD-CO , ethanol, and CO ),
Conclusions
+
-
18
Two novel zwitterionic carbamic complexes were ob-
tained by the reaction of amidines PMDBD and DBN
with CO
The crystallization of the previously reported DBU-
CO complex and the new PMDBD-CO analogue yields
2
.
(
the following procedure was adopted. Geometries were first
optimized without any constraints (except for CO , where the
bond angle was constrained to 130.0°). All calculations were
2
2
2
the respective bisamidinium bicarbonates assembled in
a hydrogen-bond network.
The elemental analysis and TGA data suggest that
23
performed using the DFT/B3LYP method and 6-311+g* basis
2
4
set within the Berny algorithm.
DBU-CO
be associated with water by hydrogen-bond interaction
involving the CO moiety. Therefore, in the crystallization
of the DBU-CO and PMDBD-CO zwitterions, a hy-
2
and PMDBD-CO
2
carbamic complexes could
(
23) (a) Becke, A. D. Phys. Rev. A 1998, 38, 3098. (b) Becke, A. D. J.
Chem. Phys. 1993, 98, 5648. (c) Lee, C.; Yang, W.; Parr, R. G. Phys.
Rev. 1998, B37, 785.
2
2
2
(24) Schlegel, H. B. J. Comput. Chem. 1982, 3, 214.
8010 J. Org. Chem., Vol. 69, No. 23, 2004

2
Activation of CO by Bicyclic Amidines
From the optimized geometries, frequency calculations were
performed to determine whether a structure is a true minimum-
energy structure with no imaginary frequency. Because it was
observed that the HOMO-LUMO gap in soft acids and bases
method27 since it was observed that the hard-soft effect
changed drastically in the presence of a solvent. All computa-
tions were performed using the Gaussian package of pro-
2
8
grams.
2
5
demanded better basis sets to be correctly described, single-
26
Acknowledgment. The authors acknowledge Pro-
fessor Ana M. de Guzzi Plepis for TGA measurements,
Dr. Silvana C. M. Agustinho for the NMR spectra
performance, Mrs. Angela Giampedro for careful En-
glish revision of the manuscript, and the Laboratorio
de Cristalografia do Instituto de F ´ı sica de S a˜ o Carlos,
Universidade de S a˜ o Paulo, for the data collection of
point calculations were performed using the B3LYP/cc-pVTZ
level of theory in order to estimate the hardness. Solvent
effects were incorporated in all calculations through the PCM
(
25) Chattaraj, P. K.; G o´ mez, B.; Chamorro, E.; Santos, J.; Fuent-
ealba, P. J. Phys. Chem. A 2001, 105, 8815.
(
26) Woon, D. E.; Dunning, T. H., Jr. J. Chem. Phys. 1993, 98, 1358.
27) (a) Miertus, S.; Scroceo, E.; Tomasi, J. Chem. Phys. 1981, 55,
(
+
-
1
17. (b) Miertus, S.; Tomasi, J. Chem. Phys. 1982, 65, 239. (c) Cossi,
bis[PMDBDH] HCO3 . They are also grateful to
FAPESP (Funda c¸ a˜ o de Apoio a Pesquisa do Estado de
S a˜ o Paulo) for the financial support given to this
research. E.R.P. is thankful for a FAPESP postdoctoral
fellowship.
M.; Barone, V.; Cameni, R.; Tomasi, J. Chem. Phys. Lett. 1996, 255,
27.
28) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.;
3
(
Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.;
Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.;
Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson,
G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.;
Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai,
H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo,
C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin,
A. J.; Cammi, R.; Pomelli, C.; Ochterski, J.; Ayala, P. Y.; Morokuma,
K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.;
Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.;
Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui,
Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.;
Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.;
Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez,
C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong,
M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision A.1; Gaussian,
Inc.: Pittsburgh, PA, 2003.
Supporting Information Available: General analytical
and compound characterization details. Crystallographic data
were deposited in the Cambridge Crystallographic Data Centre
with numbers CCDC 237594 and 237595. Crystal data and
details, as well as bond distances and angles, for DBU and
PMDBD amidinium bicarbonates are reported. The geo-
metrical parameters and the complete list of natural charges
for DBU, PMDBD, and their respective complexes with carbon
dioxide are provided. This material is available free of charge
via the Internet at http://pubs.acs.org.
JO049243Q
J. Org. Chem, Vol. 69, No. 23, 2004 8011