Bent CNN bond of diazo compounds, RR′(CN+N-)

Article abstract of DOI:10.1016/j.molstruc.2012.10.027

The reaction of ninhydrin with benzophenone hydrazone afforded 2-diazo-3-diphenylmethylenehydrazono-1-indanone 1 and 2-diazo-1,3- bis(diphenylmethylenehydrazono)indan 2. X-ray crystal structure analyses of these products showed that the diazo functional group CN⁺N ^- of 1 is bent by 172.9°, while that of 2 has a linear geometry. The crystal structure data of diazo compounds have been retrieved from the Cambridge Structural Database (CSD), which hit 177 entries to indicate that the angle of 172.9° in 1 lies in one of the most bent structures. The CSD search also indicated that diazo compounds consisting of a distorted diazo carbon tend to bend the CN⁺N^- bond. On the basis of DFT calculations (B3LYP/6-311++G(d,p)) of model compounds, it was revealed that the bending of the CNN bond is principally induced by steric factors and that the neighboring carbonyl group also plays a role in bending toward the carbonyl side owing to an electrostatic attractive interaction. The potential surface along the path of CN⁺N^- bending in 2-diazopropane shows a significantly shallow profile with only 4 kcal/mol needed to bend the CN⁺N ^- bond from 180° to 160°. Thus, the bending of the diazo group in 1 is reasonable as it is provided with all of the factors for facile bending disclosed in this investigation.

Full text of DOI:10.1016/j.molstruc.2012.10.027

Journal of Molecular Structure 1034 (2013) 346–353
Contents lists available at SciVerse ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Bent CNN bond of diazo compounds, RR0(C@N+@Nꢀ)
b
c
Motoko Akita a, Mai Takahashi a, Keiji Kobayashi a, , Naoto Hayashi , Hideyuki Tukada
⇑
a Graduate School of Science, Josai University, Sakado, Saitama 350-0295, Japan
b Graduate School of Science and Engineering, University of Toyama, Gofuku, Toyama 930-8555, Japan
c International Graduate School of Arts and Science, Yokohama City University, Seto, Kanazawa-ku, Yokohama 236-0027, Japan
h i g h l i g h t s
"
"
"
"
"
A compound bearing bent diazo group (R1A(CNN)AR2) was found.
Diazo compounds with bent bonds tend to increase their R1ACAN angles.
Bending of the diazo CNN bond is principally ascribable to steric congestion.
The
a-carbonyl group exerts attractive interaction to bend the CNN bond.
The potential surface for bending the CNN bond is significantly shallow.
a r t i c l e i n f o
a b s t r a c t
Article history:
The reaction of ninhydrin with benzophenone hydrazone afforded 2-diazo-3-diphenylmethylenehydraz-
ono-1-indanone 1 and 2-diazo-1,3-bis(diphenylmethylenehydrazono)indan 2. X-ray crystal structure
analyses of these products showed that the diazo functional group C@N+@Nꢀ of 1 is bent by 172.9°, while
that of 2 has a linear geometry. The crystal structure data of diazo compounds have been retrieved from
the Cambridge Structural Database (CSD), which hit 177 entries to indicate that the angle of 172.9° in 1
lies in one of the most bent structures. The CSD search also indicated that diazo compounds consisting of
a distorted diazo carbon tend to bend the C@N+@Nꢀ bond. On the basis of DFT calculations (B3LYP/6-
311++G(d,p)) of model compounds, it was revealed that the bending of the CNN bond is principally
induced by steric factors and that the neighboring carbonyl group also plays a role in bending toward
the carbonyl side owing to an electrostatic attractive interaction. The potential surface along the path
of C@N+@Nꢀ bending in 2-diazopropane shows a significantly shallow profile with only 4 kcal/mol
needed to bend the C@N+@Nꢀ bond from 180° to 160°. Thus, the bending of the diazo group in 1 is rea-
sonable as it is provided with all of the factors for facile bending disclosed in this investigation.
Ó 2012 Elsevier B.V. All rights reserved.
Received 5 September 2012
Received in revised form 6 October 2012
Accepted 9 October 2012
Available online 26 October 2012
Keywords:
Diazo group
Crystal structure
CSD search
DFT calculation
1. Introduction
A, B, and C. The carbon atom C1 is essentially sp2-hybridized and
both nitrogen atoms have sp hybridization: the three atoms C, N,
There has been much interest in diazoalkanes for many years
[1], because of their usefulness as precursors to carbenes, which
are intermediates in the photolysis and thermolysis of diazoalk-
anes, and more recently as a consequence of work on molecular
magnetism based on persistent triplet carbenes [2]. In contrast to
the wealth of well-established reactions of diazo compounds, the
structural aspect of these compounds has attracted much less
attention after resolving their early issue, i.e., which is the true
configuration, the acyclic (diazirine) or open configuration [3].
A common understanding of the structure of the diazo func-
tional group C1AN1AN2 is that it has a linear geometry, which is
represented by a resonance hybrid between the canonical forms
and N should have a linear geometry [4]. These structural features
are deduced from results of a number of X-ray crystallographic
analyses, in which the C1AN1 and N1AN2 bond lengths have been
mainly noted whereas the CNN angle has been little remarked on.
+
+
N
+
C
N
C
1
N
N
2
C
N
N
1
A
B
C
In the course of our study of the preparation of new p-expanded
azine compounds using the reaction of carbonyl compounds with
hydrazones, we have unexpectedly obtained the novel diazo
⇑
Corresponding author.
E-mail address: kobayak@josai.ac.jp (K. Kobayashi).
0022-2860/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.molstruc.2012.10.027

M. Akita et al. / Journal of Molecular Structure 1034 (2013) 346–353
347
compounds, 2-diazo-3-diphenylmethylenehydrazono-1-indanone
(1) and 2-diazo-1,3-bis(diphenylmethylenehydrazono)indan (2).
The structures of these products were determined by X-ray crystal-
lographic analysis. The characteristic feature observed in 1, that is,
a bent bond of the diazo C1AN1AN2 group, prompted us to search
the database of Cambridge Structural Database (CSD) for the struc-
tural outcome of diazo compounds. Herein, we report our findings
regarding the bent structure of the diazo functional group, which
has been overlooked to date.
MS (m/z): 528 + 1(16%), 306 + 1(29%), 288 + 1(14%), 153 +
1(100%). IR (KBr): 2095 (NN str.) cmꢀ1
.
2.2. X-ray crystal structure analysis
An X-ray analysis of 1 and 2 was performed using single crystals
recrystallized from acetonitrile. X-ray diffraction data were col-
lected on a Rigaku RAXIS RAPID imaging plate area detector with
graphite monochromated Mo Ka radiation (k = 0.71075 Å). Diffrac-
tion data were collected at ꢀ100 °C for both 1 and 2. The crystal
structures were solved by the direct method using SHELX97 for 1
and SIR92 for 2 and refined by the full-matrix least-squares meth-
od [5]. Non-hydrogen atoms were placed at calculated positions
with CAH = 0.95 Å and refined using the riding model. All calcula-
tions were performed using the CrystalStructure 3.8.2 crystallo-
graphic software package [6,7]. Structural parameters are listed
in Table 1.
2. Experimental
2.1. Materials and methods
A mixture of benzophenone hydrazone (0.98 g, 5.0 mmol) and
ninhydrin (1.35 g, 7.6 mmol) in methanol (50 mL) was stirred with
five drops of acetic acid at room temperature for 3 h. The mixture
was poured into water, and extracted with dichloromethane. The
combined organic phases were washed with water and brine and
dried over anhydrous MgSO4. The product mixture left after sol-
vent removal was chromatographed on a silica gel column using
dichloromethane as an eluent. Azine 3 was eluted fast, and then
compound 1 was eluted followed by compound 2. Analytically
pure 1 and 2 were isolated by further purification using gel perm-
uation chromatography (GPC, JAIGEL 1H and 2).
Crystal data and other experimental details have been depos-
ited at the Cambridge Crystallographic Data Centre (CCDC). 1:
CCDC885009. 2: CCDC885010.
2.3. Database search
Database search was carried out using CSD (version 5.33
November 2011) + 2updates [8] using the program ConQuest
(ver.1.12) [9]. The diazo group (CNN) was defined as a structural
fragment comprising of a nitrogen atom (N2) with one bond, a
nitrogen atom (N1) with two bonds, and a carbon atom (C1) with
three bonds and linked in the C1AN1AN2 sequence of these three
atoms. Thus, all canonical representations of the diazo functional
group, regardless of A, B, C, and others, are included. Then, the
CNN structure, in which the carbon atom (C1) is bonded to carbon
or hydrogen atoms such as CA(CNN)AC and CA(CNN)AH, was gen-
erated, limiting the search to organic and noncoordinating com-
pounds. The search gave 177 hits (144 crystal structures), which
dropped to 150 (125 crystal structures) after the following
1: Yield: 14%. M.p. 180–182 °C. 1H NMR (400 MHz, CD3CN): d
7.39–7.42 (2H, m), 7.44–7.53 (m, 6H), 7.56–7.58 (2H, m), 7.64–
7.68 (m, 3H), 7.76–7.79 (m, 1H). Fab-MS (m/z): 350 + 1(62%),
306 + 1(31%), 153 + 1(100%). 13C NMR (100.4 MHz, CDCl3):
d
122.5, 122.7, 127.6, 129.4, 129.2, 129.5, 130.4, 130.7, 131.3,
131.7, 133.8, 134.6, 135.9, 137.6, 138.0, 154.1, 165.9, 185.0 ppm.
IR (KBr): 2095 (NN str.), 1688 (CO str.) cmꢀ1
.
2: Yield: 8%. M.p. 210–212 °C. 1H NMR (400 MHz, CDCl3): d
7.38–7.41 (4H, m), 7.42–7.51 (14H, m), 7.53–7.57 (6H, m). 13C
NMR (100.4 MHz, CDCl3): d 120.1, 125.5, 126.4, 127.0, 127.4,
128.2, 128.5, 129.1, 132.8, 132.9, 134.7, 136.0, 153.5, 162.0 ppm.
Table 1
Crystal and experimental data of 1 and 2.
1
2
Chemical formula
Formula weight
Crystal color, habit
Crystal size
Crystal system monoclinic
Space group
C
22H14ON4
C35H24N6
528.61
Yellow platelet
0.95 ꢁ 0.10 ꢁ 0.05 mm3
Monoclinic
350.38
Yellow needle
0.30 ꢁ 0.30 ꢁ 0.05 mm3
Monoclinic
P21/a (#14)
a = 7.5248(19) Å
b = 20.239(6) Å
c = 11.665(3) Å
b = 105.621(10)°
V = 1710.9(8) Å3
4
P21/c (#14)
Lattice parameters
a = 12.586(5) Å
b = 10.896(4) Å
c = 20.377(8) Å
b = 102.611(16)°
V = 2726.9(18) Å3
4
Z value
Dcalc
F000
1.360 g/cm3
728.00
1.287 g/cm3
1104.00
Radiation
Mo K
a
(k = 0.71075 Å)
Mo Ka (k = 0.71075 Å)
l(Mo K
a)
0.871 cmꢀ1
0.785 cmꢀ1
2hmax cutoff
55.0°
55.0°
No. of reflections collected
No. of independent reflections
17512
3911
26086
6228
Residuals: R1 (I > 2.00
r(I)) 0.0457
0.036
0.048
Residuals: wR2 (I > 2.00
r
(I)) 0.1290
0.063
0.042
Goodness of fit indicator 0.765
Maximum peak in Final Diff. Map 0.27 eꢀ (Å3)
Minimum peak in Final Diff. Map ꢀ0.33 eꢀ (Å3)
Measurement
Program system
Structure determination
1.03
0.95
0.23 eꢀ (Å3)
0.50 eꢀ (Å3)
ꢀ0.19 eꢀ (Å3)
ꢀ0.48 eꢀ (Å3)
Rigaku RAXIS-RAPID
Rigaku Crystal Structure 3.8.2
Direct methods (SHELX 97)
Full-matrix least-squares on F2
CCDC885009
Rigaku RAXIS-RAPID
Rigaku Crystal Structure 3.8.2
Direct methods (SIR92)
Full-matrix least-squares on F2
CCDC885010
Refinement
CCDC deposition number

348
M. Akita et al. / Journal of Molecular Structure 1034 (2013) 346–353
filtering: (a) no crystallographic disorder and (b) an R-factor of less
than 0.1.
@NAN@ is directed toward the diazo group and adopts an s-trans
conformation to bring about a close intramolecular contact of
2.804 Å between the N atoms of the diazo and azine groups. As a
result, the azine unit C@NAN is also on the same plane of the indan
unit, while the ˜C@NA moiety derived from benzophenone hydra-
zone is slightly distorted from this plane (C@NAN@C torsion angle:
167.69°). The molecules are stacked facing this molecular plane to
2.4. DFT calculations
Optimized structures were obtained by density functional the-
ory (DFT) calculations, which were performed with the Gaussian
09 and 09 W program suites [10]. The calculations employed the
B3LYP exchange–correlation functional, which combines the
hybrid exchange functional of Becke [11,12] with the gradient-
correlation functional of Lee et al. [13]. Basis sets with polarization
functions and diffuse functions 6-311++G(d,p) were stored inter-
nally in the Gaussian 09 (09 W) program packages. The X-ray
geometries for 1 and 2 were used as a starting point for the calcu-
lations. All the optimized structures had no imaginary frequencies.
Potential energy surfaces (PESs) along a CANAN bending pathway
were calculated with a fully relaxed scan method.
form an infinite chain along the a-axis. Thus, face-to-face
-interactions are realized between neighboring molecules along
with face-to-edge -interactions using one of the phenyl rings
p,
p
p, p
of the N@C(Ph)2 moiety, which has a conformation nearly perpen-
dicular to the other phenyl ring.
3. Results and discussion
3.1. Formation of diazo compounds 1 and 2
Ninhydrin is known as a highly electrophilic compound because
of its activated ketone functional group at the 2-position [14]. It re-
acts with a variety of nucleophiles such as amines [15] as well as
phenols, and methylene compounds activated by a neighboring
carbonyl group. We have carried out the reaction of ninhydrin with
benzophenone hydrazone in acetic acid and isolated monodiazo
compound 1 in 14% yield along with tetraphenyl ketazine 3 in 8%
(Scheme 1). Compound 2 was isolated only in trace amount, being
not sufficient to characterize by spectroscopic methods, whereas
its structure could be determined on the basis of X-ray crystallo-
graphic analysis.
The reaction of ninhydrin with tosylhydrazine to afford 2-diazo-
1,3-indandione has been known as the Bamford-Stevens reaction
[16,17], while diazotization by hydrazone has rarely been encoun-
tered. It seems likely that benzophenone hydrazone reacts first at
the most electrophilic site of ninhydrin, followed by condensation
with the carbonyl group at the 1- or 3-position to give highly con-
gested bis- or tri-azine compounds, which would decompose to 1
and 2 to release steric hindrance via a process analogous to the
Bamford-Stevens reaction [18].
Fig. 1. Molecular structure of 1 with ellipsoids drawn at 50% probability level.
Table 2
Selected bond lengths (Å) and angles (°) for 1 and 2.
1
2
N1AN2
N1AC1
C1AC2
C1AC9
O1AC2
N3AC9
N3AN4
N5AN6
N2AN1AC1
N1AC1AC2
N1AC1AC9
O1AC2AC1
1.128(2)
1.319(2)
1.467(2)
1.4451(19)
1.2204(17)
1.2885(18)
1.3964(17)
1.130(3)
1.320(3)
1.463(3)
1.445(3)
3.2. X-ray crystal structure of 1 and 2
On recrystallization from acetonitrile 1 crystallizes into a mono-
clinic lattice with P21/a symmetry. The crystal data and structure
refinement of 1 are shown in Table 1. The ORTEP diagram is shown
in Fig. 1, and displacement ellipsoids are drawn at a 50% probabil-
ity level. Some selected geometric parameters are given in Table 2.
The indan skeleton of 1 is planar including the three atoms O, N,
and N attached to this ring. The NAN bond of the azine moiety
1.409(3)
1.402 (2)
179.0(2)
123.9(2)
124.7(2)
172.89(14)
120.19(12)
128.27 (14)
127.42(14)
N
N
N
+
HO OH
+
N
N
N
N
N
N
O
N
N
O
N
+
O
H2N
N
CH3COOH
2
3
1
Scheme 1. Reaction of ninhydrin with benzophenone hydrazone.

M. Akita et al. / Journal of Molecular Structure 1034 (2013) 346–353
349
The azide group plays no role in any intermolecular interaction
but only participates in intramolecular N—N contact. The N@N and
N@C distances of the diazo group are 1.128 and 1.319 Å, respec-
tively. Contrary to the assumption based on atomic radius, the
N@N bond is shorter than the N@C bond, indicating that the
N@N bond has a more pronounced multibond character than the
C@N bond. The most interesting feature in the molecular structure
of 1 is the bent bond of the diazo functional group: the C@N+@Nꢀ
bond is not in a linear geometry but is bent to 172.9° towards the
carbonyl site approximately on the same plane made by the inda-
none framework (torsion angle of O@CAC@N; 0.37°).
diagram is shown in Fig. 2. The selected bond lengths, bond angles
and torsions are listed in Table 2. The C1AN1AN2 bond is close to a
linear geometry (CNN angle: 179.0°) in contrast to that of 1. The
two azine moieties as well as the diazo group are slightly twisted
from the plane made by the indan skeleton (torsion angles of
C@NAN@C: 178.99, 177.76°), whereas the N1 atom is situated clo-
sely to two azine nitrogen atoms nearly on the same plane and
subject to intermolecular Nꢂ ꢂ ꢂN interactions with short Nꢂ ꢂ ꢂN con-
tacts (2.749 and 2.732 Å).
3.3. Cambridge Structural Database studies
The X-ray molecular structure of 2 was determined for a single
crystal obtained by recrystallization from acetonitrile. The crystal
data and structure refinement of 2 are shown in Table 1. The ORTEP
One might wonder if the bent bond of the diazo group univer-
sally occurs. Thus, we searched the Cambridge Structural Database
Table 3
Selected geometrical parameters for diazo compounds 1, 2, POXQOI, DAZFLU11, and ENIGEO computed at 6-311++G(d,p) level of theory and observed in X-ray crystallographic
analysis.
Compd.
N1AN2 (Å)
N1AC1 (Å)
C1AN1AN2 (°)
R1AC1AN1 (°)
R1AC1AN1 (°)
1
Calc.
Cryst.
1.126
1.128
1.309
1.319
172.3
172.9
120.5
120.19
128.7
128.27
2
Calc
Cryst
1.126
1.130
1.315
1.320
180
179.0
125.2
123.9
125.2
124.7
POXQOI
DAZFLU11
Calc
Cryst
1.122
1.117
1.324
1.3169
168.4
171
121.8
120.8
131.3
131.4
Calc
Cryst
1.137
1.134
1.133
1.301
1.317
1.322
180
179.44
179.43
125.5
125.5
125.47
125.02
125.3
ENIGEO
Calc
Cryst
1.139
1.146
1.309
1.313
180
178.81
116.8
117.3
116.8
116.8
114.9
N
N
N
N
+
+
+
N
N
O
CH
3
N
N
N
CH O
3
OCH
3
CH
3
POXQOI
ENIGEO
DAZFLU 11
Fig. 2. Molecular structure of 2 with ellipsoids drawn at 50% probability level.

350
M. Akita et al. / Journal of Molecular Structure 1034 (2013) 346–353
(CSD version 5.33 November 2011) for diazo compounds, restrain-
ing our search to organic and noncoordinated compounds. As de-
scribed in the experimental section, the search with restrictions,
i.e., no crystallographic disorder and an R-factor of less than 0.1,
gave 150 (125 crystal structures) hits. For these 150 hits, the scat-
ter plots of the C1AN1AN2 bond angle vs. the N1AN2 distance are
shown in Fig. 3. Inspection of the C1AN1AN2 angle in Fig. 3 indi-
cates that the angles are mostly distributed in the range of 177–
179° and an angle of 180° is observed only in three structures.
As clearly shown in Fig. 3, 1 lies in the range of the most bent
CNN bonds. We have extracted four entries with less than
174.0 Å, which are indicated by the CSD reference code (POXQUO
[19], POXQOI [19], PAFHIP [20], OBEQUJ [21]) in Fig. 3. Their struc-
tures are shown in Scheme 2, along with that of 1. Among those,
the data of POXQUO appear to be removable because of their low
reliability due to the small temperature factor of the nitrogen atom
corresponding to the N1 atom as compared with those of other
atoms. With respect to POXQOI, the result also seems to be suspi-
cious because of the lack of hydrogen atom coordinates. In any
event, the molecular structure of 1 definitely provides a new entry
of bent diazo CNN bonds that are populated sparsely in CSD.
It should be determined which direction the C@N+@Nꢀ bond is
bent to. Thus, we generated a scatter plot of the CNN angle vs. the
twist angle of N2AN1AC1AR1. In this search, the following struc-
tures were excluded: (a) structures in which the difference be-
tween the N2AN1AC1AR1 and N2AN1AC1AR2 dihedral angles,
accurately to be 180°, is less than 170°; (b) those with an
N2AN1AC1 angle of 180°. With these filters, 143 structures were
found, and for which the scatter plot of the C1AN1AN2 angle vs.
the twist angle of N2AN1AC1AR1 is shown in Fig. 4. The dihedral
angle is distributed in a wide range from 0° to 90°, although the
number of entries gradually decreases with increasing dihedral
angle. The most interesting feature is that the structure having a
large bend angle of N2AN1AC1 angle adopts a small twist angle
of N2AN1AC1AR1, that is, it bends in the plane made by N2, N1,
C1, R1, and R2. Compound 1 and the four entries in the region less
than 174° in Fig. 3 are found again in areas with low twist angles in
Fig. 4.
In 1, the intramolecular interaction between the spatially prox-
imate nitrogen atom can be observed, as judged from the contact
distance (2.804 Å), which is smaller than the sum of the van der
Waals radius (1.55 + 1.55 Å). This is also true for POXQOI and PAF-
HIP. In these compounds, the CNN group is bent toward the oppo-
site side of the interaction. The intramolecular heteroatom
interaction with the N1 atom could be partially responsible for
the bending of the C1AN1AN2 bond toward the back side of
interaction.
As shown in Figs. 3 and 4, the C1AN1AN2 bonds are more or
less bent rather than linear. Thus, the unsymmetrical structure ob-
served in the CNN bond would be related to the R1AC1AN1 and
R2AC1AN1 angles. Then, the distortion of the C1 carbon in the
R1(C1N1N2)R2 framework was investigated using a scatter plot
of the CNN angle vs. the difference between the R1AC1AN1 and
R2AC1AN1 bond angles. Fig. 5 shows that such differences in the
angles are mostly distributed in a region of less than 6°. However,
with respect to the entries that have large bent CNN angles, the
distortion is clearly pronounced compared with those of most
other cases. 1 is also part of the group of highly deformed struc-
tures showing
a difference of 8.08°. Thus, bending at the
C1AN1AN2 bond should also be affected by the distortion of the
R1AC1AN1 and R2AC1AN1 angles. This is supported by the DFT
calculations, as described in the next section.
3.4. DFT calculations
To gain more insight into the bent structure of the diazo group,
we carried out DFT calculations of various diazo compounds. First,
to confirm the reliability of the computational method adopted in
this study, we carried out calculations of diazo compounds,
namely, those with a linear diazo group (DAZFUL11 and ENI-
GEO[22]), and an extremely bent diazo group (POXQOI) as well
as for our diazo compounds 1 and 2. For all these diazo compounds,
crystallographic data are available. Selected parameters for their
optimized geometries in comparison with those of the X-ray struc-
ture are shown along with the data obtained by X-ray crystal anal-
yses for comparison in Table 3. We clearly observe from this table
the good agreement between the experimental and calculated data
for the diazo compounds, indicating the reliability of the DFT calcu-
lations adopted in this study. The N1AN2 bond in 1 and 2 is shorter
than their N1AC1 bond, which suggests predominant participation
of resonance structure B (˜CꢀAN+„N) and C (˜CꢀAN@N+) in the
structure of the diazo group. This was also supported by atomic-
centered fitting charges to electrostatic potentials calculated by
Fig. 3. Scatter plot of CNN angle vs. NAN bond length of diazo functional group.
N
N
N
+
+
2.460
170.99
N
N
O
N
172.90
N
N
CH3
CH3
+
2.804
+
N
O
173.10
172.34
N
2.888
N
O
CH3
N
O
O
O
N
N
CH3
Ph3C
COOCH3
OBEQUJ
(this study)
POXQOI
1
PAFHIP
Scheme 2. Diazo compounds having highly bent CNN bond.

M. Akita et al. / Journal of Molecular Structure 1034 (2013) 346–353
351
N2
+
N1
C1
R1
R2
for definition of the angle
R1, R2 = C or H
Fig. 4. Scatter plot of the C1AN1AN2 angle vs. twist angle of N2AN1AC1AR1.
the Breneman’s method [23]. The charges on C1, N1, and N2 are
ꢀ0.421, 0.551, and ꢀ0.269, respectively for 1 and these for 2 are
ꢀ0.347, 0.466, and ꢀ0.275, respectively.
As is evident from Table 3, the diazo group C1AN1AN2 in the
symmetric molecular structure takes a linear geometry; hence,
the N1 atom has an sp hybridization. It is therefore valid that the
N1 atom takes basically a linear geometry, but suffers deformation
due to steric and/or electronic interactions with neighboring sub-
stituents to deviate from the intrinsic position. We have also inves-
tigated the DFT optimized structures for eight model compounds
(3–10) based on the cyclopentylidenecyclopentane framework.
These compounds mimic a partial structure of POXQOI and are de-
signed with the intention to induce steric hindrance to the diazo
group by the substitution of the cyclopentylidene moiety, which
is set close to the diazo group. The results of the DFT optimized
structures are listed in Table 4, including difference in R1AC1AN1
and R2AC1AN1 bond angles, intramolecular distance between N1
and the atom (X) located most closely to N1 (X---N1), and distance
Fig. 5. Scatter plot of CNN angle vs. difference between R1AC1AN1 and R2AC1AN1
bond angles.
Table 4
Selected B3LYP/6-311++G(d,p) optimized geometries of cyclopentanylidenecyclopentanes, 3–10.
N1AN2/Å
C1AN1/Å
C1AN1AN2/°
R1AC1AN1/°
R2AC1AN1/°
D
/°
X—N1/Å
R/Å
3
4
5
6
1.145
1.131
1.144
1.129
1.294
1.312
1.295
1.310
177.2
172.2
176.6
173.4
126.6
128.4
127.2
128.8
120.8
118.0
118.7
117.5
5.8
10.4
8.5
2.776
2.684
2.692
3.083
1.69
1.16
1.60
1.38
11.3
7
8
9
10
1.131
1.121
1.131
1.128
1.308
1.326
1.307
1.311
174.5
166.7
172.7
171.9
N
128.2
131.2
130.8
130.1
118.7
115.4
115.9
116.2
9.5
15.8
14.9
13.9
2.785
2.621
2.686
3.206
1.70
1.10
1.60
1.36
N2
CH2
N
N
N1
N
C
N
N
CH3
O
3
7
5
4
6
N
N
N
N
N
N
N
O
N
Br
CH3
O
O
O
O
8
9
10
D
: Difference between R1AC1AN1 and R2AC1AN1 bond angles.
X---N1: Intramolecular distance between N1 and X, the atom located most closely to N1.
R: Distance derived by subtraction of the van der Waals radius of X from X----N1 distance.

352
M. Akita et al. / Journal of Molecular Structure 1034 (2013) 346–353
made by subtraction of the van der Waals radius of X from X----N1
distance.
In all the compounds, the neighboring cyclopentylidene group
permits the bending of the CNN bond toward the less hindered
side, regardless of the existence of the carbonyl group at this side.
Bending occurs in the plane made by cyclopentylidenecyclopen-
tane and the diazo group. Furthermore, the substituents at the 2-
position of the cyclopentylidene group (X@O, C, Br) enhance the
bending of the C1AN1AN2 bond. We can see more clearly such ste-
ric effect from Fig. 6, which shows relationship between
C1AN1AN2 bond angle and the value derived by subtraction of
the van der Waals radius of X from the distance X----N1. The latter
value was incorporated by taking into consideration that the atom-
ic volume should more accurately reflect steric congestion than the
X----N1 distance itself. Thus, on these DFT calculations, we could
assume that the origin of the bend is principally the steric
interaction.
Another interesting result is that the
(7, 8, and 9) have a tendency to bend at a larger angle than the
compounds without the -keto group (3, 4, and 5). Thus, it seems
a-keto diazocyclopentanes
Fig. 7. Relationship of C1AN1AN2 angle vs. difference in R1AC1AN1 and
R2AC1AN1 bond angles calculated for eight model compounds (3–10).
a
most likely that the carbonyl substituent on the opposite side of
steric interaction in the model compounds exerts attractive inter-
action with the diazo CNN bond, resulting in the bending of the
CNN group to this carbonyl side. As will be described later in this
section, this assumption is supported by the potential surface cal-
culations of 2-diazocyclopentanone.
As is depicted in Fig. 7, the theoretical calculations of eight
model compounds also indicate a tendency of the C1AN1AN2
bond to bend more with increasing difference in the R1AC1AN1
and R2AC1AN1 bond angles, corresponding well to Fig. 5 obtained
based by CSD retrieval.
All the above results imply that the C1AN1AN2 and R1AC1AN1
angles are readily variable depending on the structural environ-
ment. Then, for a better understanding of the nature of these sys-
tems, the potential energy surfaces (PESs) according to the bend
C1AN1AN2 angle were calculated for 2-diazopropane (11) and 2-
diazocyclopentanone (12) (Fig. 8). The optimized structure of 11
is symmetric, and its potential energies show a shallow minimum
at a linear geometry of the C1AN1AN2 bond (Fig. 8a). Upon the
change in the C1AN1AN2 bond from 180° to 160°, the potential
energy increases, but by only 4 kcal/mol.
N
N
N
+
+
N
O
CH3
CH3
12
11
The PES was also investigated for a distorted structure of 11, in
which the R1AC1AN1 angle is fixed at 130° and the R2AC1AN1 is
at 120°. Under such distortion, the potential surfaces for bending
CNN are shifted higher in energy and a potential minimum appears
at 172° on the R2AC1AN1 side (Fig. 8b). The energy surface comes
out more shallow as compared with that in the case of a symmet-
rical structure, indicating that the bent R1AC1AN1 bond facilitates
further bending of the diazo C1AN1AN2 bond. Only 2 kcal/mol is
required to bend the C1AN1AN2 bond to 160°.
The PES for 2-diazocyclopentanone (Fig. 8c) resembles that for
the distorted 2-diazopropane. A single minimum shifts to the
a-
carbonyl side at 176° with a shallow profile: only 1.2 kcal/mol is
required to bend the CNN bond from 176° to 160°. These results
are consistent with the finding from Table 4 and support the idea
Fig. 6. Relationship based on B3LYP/6-311++G(d,p) level calculations between
C1AN1AN2 bond angle and the value resulting from subtraction of the van der
Waals distance of X from the distance X----N1.
Fig. 8. Potential energy surfaces along path of bending C1AN1AN2 angle, for (a) 11
with equal angles of R1AC1AN1 and R2AC1AN1, (b) 11 with angles of
R1AC1AN1 = 130° and R2AC1AN1 = 120°, and (c) 12.

M. Akita et al. / Journal of Molecular Structure 1034 (2013) 346–353
353
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N
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Acknowledgments
This work was partially supported by a Grant-in-Aid for Scien-
tific Research (No. 21550048) from the Ministry of Education, Cul-
ture, Sports, Science and Technology, Japan.