Journal of Molecular Structure: THEOCHEM 863 (2008) 5054

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Journal of Molecular Structure: THEOCHEM

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The isomers of phenalene and their singlet and triplet states: A HartreeFock
and density functional computational investigation
Joan M. Zoellner, Robert W. Zoellner *
Department of Chemistry, Humboldt State University, One Harpst Street, Arcata, CA 95521-8299, USA

a r t i c l e i n f o a b s t r a c t

Article history: Each of the isomers of phenalene, 1H-, 2H-, 3aH-, and 9bH-phenalene, as well as the cation, neutral rad-
Received 29 April 2008 ical, and anion in the phenalenyl system, have been examined at the HartreeFock 6-31G(d) and the den-
Received in revised form 14 May 2008 sity functional B3LYP/6-31G(d) levels of theory. The structures and properties of the phenalenes were
Accepted 16 May 2008
determined as both singlets and triplets. While the data indicate that both the 9bH- and the 1H-isomer
Available online 24 May 2008
will exist as ground state singlets, the 2H- and 3aH-phenalenes are predicted to exist as ground state trip-
lets; only the synthesis of the 1H-isomer has been reported in the literature. Structurally, 1H- and 2H-
Keywords:
phenalene are planar systems, 3aH- and 9bH-phenalene are non-planar systems puckered at the satu-
Phenalene
Phenalenyl
rated carbon, and the cation, neutral radical, and anion of phenalenyl are planar D3h systems.
HartreeFock 2008 Elsevier B.V. All rights reserved.
Density functional
Isomer

1. Introduction
The non-benzenoid hydrocarbon 1H-phenalene (1), C13H10, has
been known since the molecule (then termed perinaphthindene)
was rst synthesized in low yield by Lock and Gergely [1]. Deriva-
tives were reported even earlier [2,3], and Boekelheide and Larra-
bee later reported improved syntheses of (1), termed
perinaphthene by these authors [4]. Given the structure of (1),
other isomers, (2), (3), and (4), may be envisioned, as depicted in
Fig. 1. However, only the 1H-isomer has apparently been investi-
gated; neither the 2H- nor the 3aH-isomer has been reported,
while a search of the literature reveals references [57] to the
9bH-isomer but with no denitive experimental or computational
data reported. (Careful examination of these references indicates
that the molecules reported as the 9bH-isomer may actually be re-
ports of the 1H-isomer mistakenly depicted as the 9bH-isomer.)
The presence of the saturated carbon in each of the phenalene
isomers prevents the molecules from exhibiting completely delo-
calized p-systems. In addition, isomers (2) and (3) can be reason-
ably expected to exist as ground state triplet diradicaloid
systems because of the impossibility of constructing alternating
single and double bonds to all of the unsaturated carbon atoms
in these molecules. However, in all of these isomers, the loss of
the hydrogen moiety results in the formation of a phenalenyl sys-
tem [810], C13H9. The phenalenyl system (5) itself is somewhat
unique in that phenalenyl, C13H9, can exist as a cationic 12 p-elec-
* Corresponding author. Tel.:+ 1 707 826 3244; fax:+ 1 707 826 3279.
E-mail address: rwz7001@humboldt.edu (R.W. Zoellner).
tron system [11] through the formal loss of hydride, a neutral 13 p-
electron radical [12,13] from the loss of a neutral hydrogen atom,
or a red, anionic 14 p-electron system [8,13] resulting from the loss
of a proton.
The phenalenyl moiety has been incorporated into organome-
tallic molecules as a p-donor ligand. In these systems, the ligand
may bind to a metal in an g1-mode [14], in an g3-allylic fashion
[1416], or in an g6-mode [14,17,18]. Computationally, a lithium,
calcium, or aluminium atom has been shown to form strong cova-
lent bonds to the phenalenyl moiety [19]. In addition, 1H-phena-
lene itself and derivatives of (1) have been shown to form
organometallic complexes with a variety of metals [17,18].
While a signicant amount of information is available for 1H-
phenalene and for the phenalenyl cation, neutral radical, and an-
ion, there is a dearth of information concerning the remaining
three isomers of phenalene. Herein are reported the results of Har-
treeFock and density functional computational investigations of
the structures and properties of the phenalene isomers and, for
comparison, the phenalene cation, radical, and anion system.
2. Theoretical approach
All HartreeFock calculations were carried out using both the PC
Spartan Pro computational package [20] and Gaussian 98W [21];
density functional calculations were carried out using Gaussian
98W. To assure the existence of stable minima, vibrational frequen-
cies for each molecule were determined at both the HartreeFock
and density functional levels of theory. The methods used for sin-
glet systems were RHF/6-31G(d) [22] and B3LYP/6-31G(d) [23];

0166-1280/$ - see front matter 2008 Elsevier B.V. All rights reserved.
doi:10.1016/j.theochem.2008.05.017
 J.M. Zoellner, R.W. Zoellner / Journal of Molecular Structure: THEOCHEM 863 (2008) 5054 51

H H
H
H

1H-phenalene (1) 2H-phenalene (2)

H
Fig. 2. The singlet structures of 1H-phenalene (1), left, and 9bH-phenalene (4),
3aH-phenalene (3) 9bH-phenalene (4) right. While the carbon atoms of (1) lie nearly exactly in a plane, (4) is denitely
puckered at C9b.

+,0,-

phenalenyl (5)

Fig. 1. The four possible phenalene isomers and the phenalenyl system. Note that
neither (2) nor (3) can be represented in a standard valence bond depiction except
as a set of diradicaloid resonance structures.

the corresponding UHF/6-31G(d) and UB3LYP/6-31G(d) methods

were employed for the triplet systems. No symmetry constraints
were used in any of the calculations. Fig. 3. The triplet structures of 2H-phenalene (2), left, and 3aH-phenalene (3), right.
While the carbon atoms of (2) are nearly exactly planar, (3) is denitely puckered at
3. Results and discussion C3a.

Selected calculated properties for the phenalene isomers as

both singlet and triplet molecules, as well as for the cation, neutral
radical, and anion of the phenalenyl system, are listed in Table 1.
[Complete listings of the calculated vibrational frequencies can
be found in the supplementary data, Tables S1 (phenalenes) and
S2 (phenalenyl system).] There were no signicant differences be-
tween the RHF/6-31G* results from the PC Spartan Pro package and
the RHF/6-31G(d) results from Gaussian 98W; for consistency,
however, only the Gaussian 98W results are reported herein.
For 1H-phenalene (1), the singlet is more stable than the triplet
by 125.5 kJ/mol with 6-31G(d), and by 208.4 kJ/mol with B3LYP.
The singlet is also more stable than the triplet for 9bH-phenalene
(4), by 83.8 kJ/mol with 6-31G(d) and by 22.7 kJ/mol with B3LYP.
All are stable minima on both the 6-31G(d) and the B3LYP poten-
tial energy surfaces, with all real vibrational frequencies. The sin-
glet structures of (1) and (4) are illustrated in Fig. 2.
For 2H-phenalene (2), the triplet is more stable than the singlet
by 364.4 kJ/mol at the 6-31G(d) level and by 81.1 kJ/mol at the
B3LYP level. The triplet is also more stable than the singlet for
3aH-phenalene (3), by 341.2 kJ/mol with 6-31G(d) and by
60.3 kJ/mol with B3LYP. However, at the 6-31G(d) level of theory,
although the triplet of (3) is a stable minimum on the potential en-
ergy surface, the singlet of (3) optimizes as a transition state with a
single imaginary frequency at 444.9 cm 1. All attempts to opti-
mize this molecule so as to eliminate this imaginary frequency
while maintaining the molecule as the desired isomer failed. This
frequency corresponds to the transfer of the hydrogen atom from
C3a to C1, i.e., the conversion of singlet (3) to singlet (1). In contrast,
both the singlet and the triplet states of (3) are stable minima at
the B3LYP level of theory. The triplet structures of (2) and (3) are
illustrated in Fig. 3.

Table 1
The calculated properties for the isomers of phenalene and the phenalenyl system
1
Molecule Electronic energy (a.u.) Dipole moment (D) Selected vibrational frequencies (cm , uncorrected)
HF/6-31G(d) B3LYP/6-31G(d) HF/6-31G(d) B3LYP/6-31G(d) HF/6-31G(d) B3LYP/6-31G(d)
(1)-singlet 498.12312385 501.41464841 0.5857 0.6568 3179.2, 3197.8 [m(C1AH)] 2995.6, 3008.0 [m(C1AH)]
(1)-triplet 498.07513549 501.33529083 0.3065 0.5525 3153.6, 3167.1 [m(C1AH)] 2911.6, 2920.1 [m(C1AH)]
(2)-singlet 497.98971930 501.32717919 4.2957 3.1051 3133.9, 3150,5 [m(C2AH)] 2976.2, 2986.4 [m(C2AH)]
(2)-triplet 498.12850773 501.35806668 0.3736 0.5896 3127.5, 3130.5 [m(C2AH)] 2905.8, 2920.1 [m(C2AH)]
(3)-singlet 497.97090339 501.30871809 2.6875 2.0728 2798.0 [m(C3aAH)] 2736.2 [m(C3aAH)]
(3)-triplet 498.10084164 501.33169626 0.2343 0.3597 2962.2 [m(C3aAH)] 2714.3 [m(C3aAH)]
(4)-singlet 498.04215420 501.33607021 0.1345 0.1823 3047.4 [m(C9bAH)] 2810.4 [m(C9bAH)]
(4)-triplet 498.01024022 501.32741796 0.0188 0.0694 2818.0 [m(C9bAH)] 2727.4 [m(C9bAH)]
(5)-cation 497.34179328 500.58787202
(5)-radical 497.58376907 500.81065657 0.0000 0.0000
(5)-anion 497.52903049 500.84086927
52 J.M. Zoellner, R.W. Zoellner / Journal of Molecular Structure: THEOCHEM 863 (2008) 5054

The greater stability of the triplet state of (2) when compared to

. H
H
. H
H
. .
. H
(2) triplet ( 3) triplet
Fig. 4. The triplet ground states for (2) and (3) redrawn to represent some of the
aromatic resonance structures possible for each isomer.
The electronic energies at the B3LYP/6-31G(d) level of theory
indicate that for the ground state molecules, (1) singlet is the most
stable system, followed by (2) triplet, (4) singlet, and (3) triplet.
Such an ordering might seem unusual in that the triplet system
of (2) is predicted to be signicantly (57.8 kJ/mol) more stable than
the singlet system of (4). However, the structure of (4) may be con-
sidered as a perimeter of six conjugated carboncarbon double
bonds with a saturated carbon atom in the center, similar to
trans-15,16-dimethyl- and trans-15,16-diethyl-dihydropyrene,
molecules with two saturated carbon atoms surrounded by perim-
eters of seven conjugated carboncarbon double bonds [24]. In the
dihydropyrene molecules, the perimeters are Hckel (4n + 2) 14 p-
electron aromatic systems, but in (4), the perimeter is formally a
12 p-electron system and thus Hckel (4n) anti-aromatic (See
Fig. 1). Thus, the synthesis of singlet (4) may not be quite as
straight-forward as that of singlet (1).
(3) may be due to the structural potential for aromatic stabilization
within the systems [25]. As shown in Fig. 4, (2) can be represented
. as a naphthalene-type moiety fused to the ring containing the
diradical and the saturated carbon, while in (3), only a fused ben-
zene-type moiety can be produced, and that system is forced to be
locked into a single ring in (3). Thus (2), with the greater number of
aromatic resonance structures, is expected to be more stable than
(3), as is the case at both the HartreeFock and density functional
levels of theory.
Selected structural parameters for the ground state phenalene
structures (1) and (4) as singlets and (2) and (3) as triplets
are listed in Table 2. [Cartesian coordinates for all molecules can
be found in the supplementary data, Tables S3 (phenalenes) and
S4 (phenalenyl system).] Singlet (1) and triplet (2) are nearly per-
fectly planar molecules, with torsion angles exhibiting less than
0.5 deviation from planarity, while triplet (3) and singlet (4) exhi-
bit signicant puckering at the nominally sp3-hybridized carbon
atom. Although all molecules were optimized without symmetry
constraints, (1) and (3) closely approximately Cs-symmetry, while
(2) and (4) approximate C2v- and C3v-symmetry, respectively.
Carboncarbon bond distances in the phenalenes are, on the
whole, unremarkable, especially when considered in the context
of the preceding discussion. The bond distances adjacent to the
sp3-hybridized carbon atom are approximately 1.501.52 , as ex-
pected for sp3sp2 CAC bonds. Little CAC bond alternation is ob-
served in singlet (1) or triplet (2); both molecules appear to be
best described as naphthalene-like systems fused to a partially-sat-

Table 2
Selected calculated structural parameters for the ground state isomers of phenalene

Parameter 1H-phenalene (1) singlet 2H-phenalene (2) triplet 3aH-phenalene (3) triplet 9bH-phenalene (4) singlet
RHF/6-31G(d) B3LYP/6-31G(d) UHF/6-31G(d) B3LYP/6-31G(d) UHF/6-31G(d) B3LYP/6-31G(d) RHF/6-31G(d) B3LYP/6-31G(d)
r(C1AC2) 1.5026 1.5028 1.5007 1.4965 1.4133 1.4102 1.4675 1.4560
r(C2AC3) 1.3212 1.3402 1.5007 1.4965 1.3771 1.3713 1.3303 1.3545
r(C3AC3a) 1.4692 1.4599 1.3975 1.3953 1.5076 1.5068 1.4663 1.4550
r(C3aAC9b) 1.4318 1.4353 1.4422 1.4444 1.5172 1.5183 1.5176 1.5203
r(C9aAC9b) 1.4227 1.4252 1.4422 1.4444 1.4206 1.4161 1.5175 1.5204
r(C1AC9a) 1.5175 1.5194 1.3975 1.3953 1.4277 1.4323 1.3311 1.3559
r(C3aAC4) 1.3619 1.3840 1.4268 1.4245 1.5076 1.5068 1.3311 1.3558
r(C4AC5) 1.4163 1.4139 1.3951 1.3915 1.3771 1.3713 1.4675 1.4560
r(C5AC6) 1.3553 1.3751 1.3984 1.3927 1.4133 1.4102 1.3303 1.3545
r(C6AC6a) 1.4243 1.4239 1.4217 1.4219 1.4277 1.4323 1.4663 1.4552
r(C6aAC9b) 1.4085 1.4319 1.4264 1.4230 1.4206 1.4161 1.5175 1.5203
r(C6aAC7) 1.4154 1.4175 1.4217 1.4219 1.4203 1.4174 1.3311 1.3558
r(C7AC8) 1.3601 1.3777 1.3984 1.3927 1.3968 1.3927 1.4675 1.4560
r(C8AC9) 1.4096 1.4106 1.3951 1.3915 1.3968 1.3927 1.3303 1.3545
r(C9AC9a) 1.3654 1.3840 1.4268 1.4245 1.4203 1.4174 1.4663 1.4551
r(C1AH) 1.0886 1.1021 1.0765 1.0877 1.0755 1.0865 1.0763 1.0877
r(C2AH) 1.0766 1.0880 1.0926 1.1086 1.0761 1.0878 1.0756 1.0870
r(C3AH) 1.0763 1.0885 1.0765 1.0877 1.0760 1.0871 1.0758 1.0876
r(C3aAH) 1.1030 1.1228
r(C4AH) 1.0760 1.0878 1.0757 1.0872 1.0760 1.0871 1.0763 1.0877
r(C5AH) 1.0754 1.0868 1.0754 1.0870 1.0761 1.0878 1.0756 1.0870
r(C6AH) 1.0758 1.0875 1.0756 1.0869 1.0755 1.0865 1.0758 1.0876
r(C7AH) 1.0758 1.0875 1.0756 1.0869 1.0758 1.0872 1.0763 1.0877
r(C8AH) 1.0755 1.0870 1.0754 1.0870 1.0754 1.0869 1.0756 1.0870
r(C9AH) 1.0769 1.0884 1.0757 1.0872 1.0758 1.0872 1.0758 1.0876
r(C9bAH) 1.0997 1.1174
\(C9aAC1AC2) 114.2566 114.4968 123.2754 123.1645 120.8322 120.8030 121.4217 121.4225
\(C1AC2AC3) 123.3125 122.8069 113.1016 113.4846 121.2817 121.5356 121.4981 121.6249
\(C2AC3AC3a) 122.3414 122.4376 123.2754 123.1645 120.7740 120.6362 120.8492 121.0699
\(C3AC3aAC9b) 118.5466 118.6985 120.2574 120.2351 112.4220 112.9611 116.5539 116.8603
\(C3AC3aAC4) 121.7321 121.7670 121.4019 121.6788 114.6523 115.6094 123.3397 123.6879
\(C3aAC9bAC9a) 120.8922 120.9831 119.8329 119.7162 119.7652 119.6745 113.6822 114.6350
\(C9bAC9aAC1) 120.6434 120.5630 120.2573 120.2351 119.3236 119.3396 119.9951 119.3191
\(C2AC1AC9aAC9) 179.8583 178.9109 179.9745 179.9780 171.2475 170.3836 177.7793 177.0313
\(C3AC2AC1AC9a) 0.1559 1.3465 0.0549 0.0487 7.7943 8.3960 7.3372 5.8119
\(C3AC3aAC4AC5) 179.9697 179.5838 179.9975 179.9971 153.9432 154.8756 177.8037 179.9996
\(C3aAC9bAC9aAC9) 179.9466 179.7143 179.9915 179.9915 170.5768 172.0634 160.3170 161.4396
 J.M. Zoellner, R.W. Zoellner / Journal of Molecular Structure: THEOCHEM 863 (2008) 5054 53

Table 3
Selected calculated structural parameters for the phenalenyl system

Parameter Phenalenyl (5) cation Phenalenyl (5) neutral radical 3aH-Phenalene (3) anion
RHF/6-31G(d) B3LYP/6-31G(d) UHF/6-31G(d) B3LYP/6-31G(d) RHF/6-31G(d) B3LYP/6-31G(d)
r(C1AC2) 1.3839 1.3938 1.3966 1.3926 1.3804 1.3919
r(C3AC3a) 1.4088 1.4170 1.4196 1.4185 1.4142 1.4216
r(C3aAC9b) 1.4110 1.4222 1.4305 1.4312 1.4347 1.4430
\(C1AC2AC3) 119.5424 119.8935 120.5745 120.7322 122.4100 121.7105
\(C2AC3AC3a) 121.2963 121.0738 120.7560 120.8072 120.1225 120.5206
\(C3AC3aAC9b) 118.9326 118.9810 118.9568 118.8241 118.6726 118.6212
\(C3aAC9bAC9a) 120.0000 119.9967 120.0000 120.0044 119.9998 120.0023
\(C2AC1AC9aAC9) 179.9994 179.9999 179.9998 179.9999 179.9996 179.9984
\(C3AC2AC1AC9a) 0.0002 0.0000 0.0003 0.0007 0.0000 0.0015
\(C3aAC9bAC9aAC9) 179.9995 179.9998 179.9997 179.9985 179.9996 179.9983

+,0,- 4. Conclusions

The four phenalene isomers, 1H-phenalene (1), 2H-phenalene

phenalenyl (5)
Fig. 5. A depiction of the phenalenyl system as a delocalized 12p-electron
surrounding a central carbon atom.
urated ring system containing the sp3-carbon atom at either C1 or
C2, respectively. In a similar fashion, triplet (3) appears to be best
described as a benzene-like system fused to a two-ring system
with an sp3-carbon atom at C3a.
When compared to the other isomers of phenalene, (4)
exhibits signicant CAC bond alternation in the perimeter
carbon system that circles the central sp3-carbon atom at
C9b, with short bonds of approximately 1.35 alternating
with longer bonds of approximately 1.46 . Such a calculated
structure highlights the potentially anti-aromatic character of
the molecule and underscores the description of the mole-
cule as a 12 p-electron perimeter surrounding the central
carbon atom.
In contrast to the signicant structural differences observed in
the isomers of phenalene, the structures (Table 3) of the phenale-
nyl cation, neutral radical, and anion (5) are very similar, being
nearly exactly planar (torsion angles with less than 0.001 devia-
tion from planarity) and exhibiting nearly perfect D3h symmetry.
No bond alternation is observed. However, at the B3LYP/6-31G(d)
level of theory, some trends in bond lengths can be noted: When
comparing, in order, the cation, neutral radical, and anion of the
phenalenyl system, C1AC2 is observed to shorten slightly, C3AC3a
to lengthen slightly, and C3aAC9b to lengthen to a somewhat great-
er extent as the charge on the system changes from positive to
neutral to negative.
The phenalenyl cation, neutral radical, and anion each appear
to be best described as a delocalized 12 p-electron periphery sur-
rounding a central carbon atom, as opposed to singlet (4),
wherein the 12 p-electron periphery exhibited signicant CAC
bond alternation. Thus, rather than depicting (5) as in Fig. 1, a
more accurate picture of this system may be that shown in
Fig. 5. The calculated Mullikan charges on the central carbon
atom (C9b) are positive for the phenalenyl cation (+0.021 e), neg-
ative for the neutral radical ( 0.020 e) and negative for the an-
ion ( 0.061 e). The three carbon atoms (C3a) adjacent to the
central carbon atom have positive Mullikan charges, and the
Mullikan charges for the remaining carbon atoms (C1, C2) are
negative, in each of these phenalenyl systems.
(2), 3aH-phenalene (3), and 9bH-phenalene (4), have been studied
computationally at both the HartreeFock 631G(d) and the den-
sity functional B3LYP/6-31G(d) levels of theory as both singlet
and triplet state molecules. Both (1) and (4) are predicted to be
ground state singlets, while (2) and (3) are calculated to be ground
state triplets. While singlet (1), the only isomer synthesized to
date, is calculated to be the most stable, triplet (2) is also predicted
to be a potentially-synthesizable target. Singlet (4) may be best de-
scribed as an anti-aromatic 12 p-electron periphery of alternating
conjugated single and double bonds surrounding a central sp3-car-
bon atom, while the phenalenyl cation, neutral radical, and anion
appear to be composed of a delocalized 12 p-electron periphery
surrounding a central carbon atom.
Acknowledgements
The authors acknowledge the National Science Foundations
Course, Curriculum, and Laboratory Improvement Program, Adap-
tation and Implementation Section (NSF-9950344) for generous
support for the initial purchase of computers and computational
chemistry software. Matching funds and additional support have
been received from the Humboldt State University Department of
Chemistry, the College of Natural Resources and Sciences, the Of-
ce for Research and Graduate Studies, the Ofce of the Vice-Pres-
ident for Academic Affairs, and the Ofce of the President, as well
as from the Humboldt State University Sponsored Programs Foun-
dation. One of us (J.M.Z.) also acknowledges the receipt of a Hum-
boldt Chemistry Clark Research Scholarship.
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.theochem.2008.05.017.
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