XRD studies, vibrational spectra, andmolecular structure of 1h-imidazo [4,5-b]pyridine based on DFT quantum chemical calculations

Article abstract of DOI:10.1002/jrs.2552

The molecular structures and vibrational properties of 1H-imidazo[4,5-b]pyridine in its monomeric and dimeric forms are analyzed and compared to the experimental results derived from the X-ray diffraction (XRD), infrared (IR), and Raman studies. The theoretical data are discussed on the basis of density functional theory (DFT) quantum chemical calculations using Lee-Yang-Parr correlation functional (B3LYP) and 6-31G(d,p) basis. This compound crystallizes in orthorhombic structure, space group Pna2₁(C_2v⁹) and Z = 4. The planar conformation of the skeleton and presence of the N-H· · ·N hydrogen bond was found to be characteristic for the studied system. The temperature dependence of IR and Raman modes was studied in the range 4-294 K and 8-295 K, respectively. The normal modes, which are unique for the imidazopyridine derivatives are identified.

Full text of DOI:10.1002/jrs.2552

Research Article
Received: 6 October 2008
Accepted: 27 October 2009
Published online in Wiley Online Library: 22 December 2009
(wileyonlinelibrary.com) DOI 10.1002/jrs.2552
XRD studies, vibrational spectra,
and molecular structure of 1H-imidazo
[
4,5-b]pyridine based on DFT quantum
chemical calculations
L. Dymi n´ ska, A. G a¸ gor, M. M a¸ czka, Z. W e¸ gli n´ ski and J. Hanuza
a
b
c
a
a,c∗
The molecular structures and vibrational properties of 1H-imidazo[4,5-b]pyridine in its monomeric and dimeric forms are
analyzed and compared to the experimental results derived from the X-ray diffraction (XRD), infrared (IR), and Raman studies.
The theoretical data are discussed on the basis of density functional theory (DFT) quantum chemical calculations using
Lee–Yang–Parr correlation functional (B3LYP) and 6-31G(d,p) basis. This compound crystallizes in orthorhombic structure,
9
space group Pna21(C2v ) and Z = 4. The planar conformation of the skeleton and presence of the N–H· · ·N hydrogen bond
was found to be characteristic for the studied system. The temperature dependence of IR and Raman modes was studied in
the range 4–294 K and 8–295 K, respectively. The normal modes, which are unique for the imidazopyridine derivatives are
identified. Copyright ꢀc 2009 John Wiley & Sons, Ltd.
hK ye dy rwo og re dn s b: oi mn idd azopyridine; quantum chemical calculations; crystal and molecular structure; infrared and Raman spectra; N–H· · ·N
Introduction
structural and vibrational properties are possible. Therefore, the
present article compares the results of the X-ray diffraction (XRD)
studies with those obtained from the molecular optimization, as
well as infrared (IR) and Raman spectra recorded for the solid state
with the theoretical calculations. The normal modes character-
istic for the 1HIPb skeleton and the HBs in this system are also
discussed.
Purine is one of the most frequently investigated aza analogue of
benzimidazole. Purineanditsderivativesfindpotentialapplication
as chemical–biology tools and therapeutic agents. In particular,
compounds structurally related to the intracellular modulator
adenosine have been shown to possess biological activity as
[
1]
[2]
adenosine receptor ligands, antiviral and antitumor agents,
and enzyme inhibitors. This is even more true for deazapurine
[
3]
derivatives. For example, 1-deazapurine (imidazo[4,5-b]pyridine) Experimental
derivatives were demonstrated to exhibit in vivo activity against
mouse leukemia.[ The 1-deazapurine nucleosides were shown
4]
Synthesis
to exhibit antitumor, anti-HIV-1, cytotoxicity and inhibition of
IPb of 99% purity was purchased from Aldrich. This product has
been compared to the single crystal obtained by us using a
new synthesis method. We used 2,3-diaminopyridine as a starting
substrate. Two grams of 2,3-diaminopyridine were dissolved in
[
5,6]
adenosine deaminase activities.
The 1-deazapurine derivatives
are also considered as candidates for components of unnatural
base pairs.[ It is believed that creation of unnatural base pairs for
the expansion of the genetic alphabet and code would allow us
to incorporate various unnatural components into nucleic acids
and proteins at desired positions, to develop novel functional
biopolymers.[
7]
4
0 ml of 100% formic acid and the reaction mixture was boiled
under reflux for 6 h. When formic acid was evaporated under
8]
The crucial question of above reviewed studies is to have the
tool that allows us to characterize the structure of the skeleton,
type of isomerization, as well as the type of hydrogen bond
∗
Correspondenceto:J. Hanuza,DepartmentofBioorganicChemistry,Instituteof
ChemistryandFoodTechnology,FacultyofEngineeringandEconomy,Wrocław
University of Economics, 118/120 Komandorska Str., 53-345 Wrocław, Poland.
E-mail: J.Hanuza@int.pan.wroc.pl
(
HB) appearing in the imidazopyridine (IP) derivatives. In our pre-
vious article on molecular structures, vibrational energy levels
and potential energy distributions of 1H-imidazo[4,5-b]pyridine
a Department of Bioorganic Chemistry, Institute of Chemistry and Food
Technology, Faculty of Engineering and Economy, Wrocław University of
Economics, 118/120 Komandorska Str., 53-345 Wrocław, Poland
(1HIPb), 3H-imidazo[4,5-b]pyridine, 5-methyl-1H-imidazo[4,5-
b]pyridine (5MIPb), 6-methyl-1H-imidazo[4,5-b]pyridine, and 7-
[
9]
b Department of Crystallography, Institute of Low Temperature and Structure
Research, Polish Academy of Sciences, Wrocław, Poland
methyl-3H-imidazo[4,5-b]pyridine were studied. For our pre-
vious article we did not have the crystallographic data on the
non-substituted 1HIPb, but the single crystal of this compound
has been obtained by us and more precise discussion of the
c Department of Solid State Spectroscopy, Institute of Low Temperature and
Structure Research, Polish Academy of Sciences, Wrocław, Poland
J. Raman Spectrosc. 2010, 41, 1021–1029
Copyright ꢀc 2009 John Wiley & Sons, Ltd.

L. Dymi n´ ska et al.
[
23]
reduced pressure, the next portion of 40 ml formic acid was
added, the reaction mixture was boiled under reflux for 4 h, and
the formic acid was again evaporated under reduced pressure.
Then 3.5 g of solid KHCO3 was added to the obtained mixture and
have been corrected using the RAINT computer program based
[
25]
on Ref. [24]. The AniMol program was used for visualization of
the vibrational normal modes and BALGA program[ was used for
estimationofthepotentialenergydistribution(PED)contributions
of the internal coordinates to the normal modes.
26]
◦
everything wasdriedat140 Cfor5 h. Then20 mlwaterwasadded
to the mixture, the obtained solution was evaporated to dryness
◦
under reduced pressure, and the residue was dried at 110 C for
4
X-ray studies of IPb
h. The solid product was extracted with absolute alcohol, boiled
with active carbon, and then evaporated to dryness. Then 50 ml
of ethyl acetate and a few milliliters of nitryl acetate are added to
the residue, it is boiled, and another portion of active carbon was
added. The solution was filtered off and left for 72 h in refrigerator.
Crystallographic data were collected at 295 K on X-calibur
diffractometer with CCD detector and graphite-monochromated
Mo Kα radiation (λ = 0.71073 Å). The CrysAlis software version
1.170.32[ was used for data processing. An empirical absorption
correction was applied using spherical harmonics implemented
in SCALE3 ABSPACK scaling algorithm. The structure was solved
by direct methods and refined by the full-matrix least-squares
27]
The product was re-crystallized from ethyl acetate and dried at
◦
1
10 C. The yield of the IPb was 1.6 g, i.e. 73.4% and its melting
◦
point 148.6 C. The result of the chemical analysis for the C6H5N3
composition was as follows: C 60.04, H 4.41, N 35.10 wt%, which
is in good agreement with the expected composition (C 60.47, H
2
[28]
method against F by means of SHELX–97 program package.
All non-hydrogen atoms were refined anisotropically. Positions of
all H atoms were taken from difference-Fourier maps and refined
isotropically. The isotropic displacement parameters Uiso(H) were
constrained to be xUeq(carrier atom), where x = 1.2.
4
.23, N 35.3 wt%). To obtain the single crystals of this compound
the powder was dissolved in the ethyl alcohol and very slowly
◦
vaporized at about 5 C in the refrigerator. The method proposed
by us allows us to obtain the single crystal samples suitable to the
XRD studies.The following reaction pathways have been used in
the synthesis of IPb.
Crystal data of IP
C6H5N3, Mr = 119.13, orthorhombic, space group Pna21, Z =
4
5
, a = 14.6548(16), b = 9.4587(7), c = 3.9403(4) Å, U =
NO2
3
46.19(9) Å , 6364 reflections measured, 1303 unique (Rint =
HNO3
H SO
2
2
2
2
4
0.108). The final R(F > 2σ(F )), wR(F ) values were 0.035 and 0.06,
4
respectively. The final coordinates x, y, z of the heavy atoms (×10 )
N
NH2
N
N
NH2
NH-NO2
were: N(1) 7691(1), 4289(1), 8406(4); C(2) 7164(1), 3361(2), 6689(5);
N(3) 7524(1), 2099(2), 6414(4); N(4) 8968(1), 1183(1), 8459(5);
C(5) 9716(1), 1576(2), 0091(5); C(6) 9886(1), 2908(2), 1414(6);
H
NH2
N
C(7) 9241(2), 3956(2), 1087(6); C(8) 8467(2), 3586(2), 9340(6); C(9)
red.
HCOOH
NH2
[29]
8
351(1), 2219(2), 8094(5).
N
N
N
Results and Discussion
IR and Raman measurements
Fourier transform (FT)-IR spectra were measured in the
X-ray structure of IPb
−
1
4
000–30 cm range with a BIORAD 575 spectrophotometer. The
In the crystal of IPb, one molecule is found in the asymmetric
unit with all atoms located in general positions. Figure 1(a) shows
the molecular structure along with the atom-labeling scheme.
The conformation of the molecule is almost planar. The highest
deviation from the mean plane that passes through all atoms
concerns C6 atom and is equal to 0.014(2) Å, the planes of
imidazole and pyridine rings intersect at an angle of 1 . The
structure of IPb molecule is similar to that of 5MIPb.[ The pyridine
ringisdistorted.Thevalenceanglesbetweennon-hydrogenatoms
of pyridine are in the range of 115.52(18)–125.90(18) , whereas
spectra were obtained and compared for the KBr pellets as well
as Nujol and fluorolube mulls. FT-Raman spectra were recorded
−
1
in the 4000–80 cm range with a BRUKER 110/S spectrometer.
The 1064-nm line of an Nd : YAG laser was used as excitation. The
−
1
resolution was 2 cm , both in Raman and IR studies.
◦
BothIRandRamanspectraofthecommerciallyavailableIPband
the one synthesized by us with the new procedure are identical.
The low temperature studies were performed in the range
9]
◦
4
–294 K for the IR spectra and 8–295 K for the Raman spectra
using Janis ST100 Cryostat (USA).
the inter-atomic distances assume intermediate values between
those for single and double bonds. In imidazole ring the C2–N1
and C2–N3 bond lengths differ in 0.04 Å (1.350(2) and 1.310(2)
Å, respectively) that indicates non-uniform distribution of charge
over both N atoms.
Chemical quantum calculations
The molecular structures of the compounds studied were
optimized at the density functional theory (DFT) level using
The key features of the crystal structure packing are inter-
molecular short N–H· · ·N contacts. They are formed between the
nitrogen from neighboring imidazole ring. The N1 nitrogen is a
donor of hydrogen, whereas the second nitrogen N3 serves as
an acceptor with the donor acceptor distance of 2.928(2) Å. The
hydrogen acceptor distance is 2.140(15) Å and the angle ∠ donor
[
10–12]
the Lee–Yang–Parr correlation functional (B3LYP)
and 6-
13–19]
3
1G(d,p) basis.[
Raman and IR wavenumbers as well as
the band intensities were calculated at the same DFT level
using the GAUSSIAN 98W program.[20] The calculated and
experimental values were compared using the scaling factors (SF)
method[
21,22]
tocorrecttheevaluatedwavenumbersforvibrational
hydrogen acceptor (DNA) is 159(2) . This way ribbons of molecules
◦
anharmonicity and deficiencies inherent to the computational
level used. The intensities of the Raman lines in theoretical spectra
expanding along [011] direction are produced. The dihedral an-
gle between two molecular planes in a ribbon is 51.17 . Figure 2
◦
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J. Raman Spectrosc. 2010, 41, 1021–1029

DFT quantum chemical calculations of 1H-imidazo[4,5-b]pyridine
is a common feature in parallel, stacked aromatic systems.[30]
The displacement of pyridine ring centers is equal to 2.0 Å,
whereas the separation of pyridine and imidazole centers is equal
to 1.5 Å.
Molecular structure of the IPb dimer and monomer
The structural parameters obtained from the geometry optimiza-
tion of the IPb in the monomeric and dimeric forms are listed in
Table 1 together with the X-ray data of the IPb and IP derivative: 5-
methyl-1H-imidazo[4,5-b]pyridine (1H-5MIPb) previously studied
by us.[ The atom numbering scheme used in the calculations is
given in Fig. 1(a).
9]
Table 1 shows that the bond lengths and angles calculated for
the 1HIPb monomer and IPb dimer are in good agreement with
the experimental XRD values obtained for 1H-5MIPb[ and IPb.
The largest difference between experimental and calculated bond
9]
◦
lengths and angles is 0.07 Å and 6.39 , respectively.
Normal modes of the IPb monomer and dimer
The calculated and experimental wavenumbers of IPb dimer and
1
HIPb monomer are shown in Table 2 where the PED data are
also presented. The corresponding theoretical and experimental
spectra are presented in Figs 3 and 4.
There are 78 vibrational degrees of freedom for IPb dimer: 53
normal modes correspond to the in-plane and 25 modes to the
out-of-plane modes. On the other hand, the 1HIPb monomer of
the formula C6H5N3 has 36 vibrational degrees of freedom: 15
normal modes correspond to stretching modes [ν(NH), 4 ν(CH),
and 10 ν(φ)] and 21 bending modes can be subdivided into 10
in-plane and 11 out-of-plane modes. All normal modes of the
IPb monomer could be subdivided into the vibrations in which
only the pyridine ring is involved, the vibrations in which only
the imidazole ring participates, and the modes of the mixed
nature, in which both rings vibrate in the concerted motion.
For the dimer the coupling of two IPb units through the HB
leads to the splitting of these vibrations into two components
with nearly the same wavenumbers and PED contributions
Figure 1. (a) X-ray data for the IPb monomeric unit. (b) Molecular model
used in the DFT calculations.
(Table 2).
The nine-atomic skeleton of the IPb gives rise to the 21 normal
modes: 14 of them are characteristic for this system and can be
used as the diagnostic vibrations of the IP systems appearing
in the pharmaceuticals. These vibrations are presented in Fig. 5,
where the calculated and experimental wavenumbers are given. It
should be noted that for all these normal modes strong or medium
intensity bands are observed in the IR or Raman spectra. The ν(ꢀ)
−
1
stretching vibrations are observed in the 250–1624 cm range
ꢀdenotesthewholeIPskeleton, i.e. φ +φ system). Among them
(
P
I
the in-plane vibrations are observed at 1622 (IR), 1581 (RS), 1507
(
7
RS), 1386 (RS), 1344 (IR, RS), 1278 (IR), 1279 (RS), 1043 (RS), 777 (IR),
81 (RS), 622 (IR), 554 (RS), and 452 cm (IR). On the other hand,
−
1
Figure 2. The projection of IPb crystal packing along c direction.
the characteristic out-of-plane vibrations of the IP skeleton are
−
1
observed at 790 (IR), 643 (RS), 588 (IR), and 250 cm (IR, RS). The
vector description of these modes is shown in Fig. 5. They could
be divided into nearly pure vibrations of the pyridine or imidazole
ring or mixed vibrations of the both rings. The modes calculated at
presents the crystal packing of IPb as well as HBs existing in the
system under study.
It is worth noting that additional intermolecular interaction
appears to generate the crystal structure, i.e. π –π interactions
that are present within the molecules stacking in c direction.
The adjacent molecules are arranged parallel to each other
with the ring separation of 3.38 Å. To minimize the repulsive
π electron forces, the centers of molecules are shifted and this
−
1
−1
912 cm for the monomer and at 925 and 909 cm for the dimer
are examples of nearly pure imidazole ring vibrations: δ(φ ). The
I
−
1
mode calculated at about 545 cm is an example of the nearly
pure pyridine ring vibration: δ(φ ). The δ(φ ) mode is observed at
P
P
−
1
554–560 cm in the experimental spectra. The other vibrations
J. Raman Spectrosc. 2010, 41, 1021–1029
Copyright ꢀc 2009 John Wiley & Sons, Ltd.
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L. Dymi n´ ska et al.
Table 1. Comparison of the calculated geometrical parameters for 1HIPb monomer and IPb dimer with experimental X-ray data obtained by us for
IPb and for 1H-5MIPb[
9]
Optimized parameters from DFT data B3LYP 6-31G(d,p)
◦
1H-5MIPb[9]
Bond lengths (Å), angles ( )
1HIPb monomer
IPb dimer
Crystal structure of IPb
N1–C2
1.380
1.380
1.374
1.376
1.373
1.382
1.310
1.388
1.335
1.336
1.409
1.392
1.392
1.417
1.350
1.368
1.310
1.385
1.325
1.341
1.386
1.376
1.372
1.394
107.2
113.8
103.8
113.8
125.9
119.8
115.5
121.0
104.7
123.9
110.6
1.349
1.380
N1–C8
C2–N3
1.307
1.312
1.314
N3–C9
1.388
1.385
1.378
N4–C5
1.335
1.335
1.337
N4–C9
1.337
1.338
1.352
C5–C6
1.409
1.408
1.394
C6–C7
1.393
1.393
1.376
C7–C8
1.391
1.392
1.375
C8–C9
1.421
1.425
1.390
C2–N1–C8
N3–C2–N1
C2–N3–C9
C5–N4–C9
N4–C5–C6
C7–C6–C5
C6–C7–C8
C7–C8–C9
N1–C8–C9
N4–C9–C8
N3–C9–C8
106.42
114.04
104.51
115.20
124.90
120.22
115.25
120.64
104.68
123.79
110.35
106.79
114.50
104.16
115.23
124.94
120.13
115.53
120.35
105.00
123.80
110.17
106.79
113.54
104.89
115.10
124.60
120.43
115.23
120.38
104.71
124.25
110.08
105.70
115.00
103.11
115.21
123.10
121.10
116.52
119.50
105.16
124.51
111.03
N–H· · ·N
3.034
2.928(2)
159(2)
∠
(N–H· · ·N)
167.16
Table 2. Experimental and scaled wavenumbers (in cm 1) of the vibrational spectra for IPb monomer and dimer (calculated values were scaled
−
using the factors: 0.96 for ν1 –ν5 and 0.97 for ν6 –ν36)
Experimental wavenumbers
Calculated wavenumbers
IPb
PED contributions
IPb
νn
IR
RS
Monomer
Dimer
Monomer
100 ν(NH)
Dimer
ν1
ν2
ν3
ν4
ν5
3475 b
3093 m
3083 m
3065 m
3029 m
3519
3120
3082
3064
3040
3522
100 ν(NHI)
3119 m
3095 vw
3061 m
3038 w
3131
99 ν(CH)I
96 ν(CH)P
98 ν(CH)P
95 ν(CH)P
100 ν(CH)I
96 ν(CH)P
97 ν(CH)P
96 ν(CH)P
3090, 3077
3071, 3057
3055, 3031
2985 vw
2980–2500
s, vb
3288
100 ν(NHB): stretching
ν(N–H· · ·N) HB vibration
ν6
ν7
ν8
1622 m
1578 w
1506 vw
1623 vw
1581 m
1507 m
1624
1568
1505
1627, 1622
1574, 1566
1511, 1505
50 ν(φ ) + 16 ν(φ )
40 ν(φ ) + 13 ν(φ )
P
I
P
I
77 ν(φ )
55 ν(φ ) + 17 ν(φ , φ )
P
P
P
I
47 ν[φ (C N)I]
33 ν[φ (C N)]
I
I
+
10 ν(φ ) + 14 δ(CH)I
+ 12 δ(CH)I + 10 δ(NHB)
P
ν9
1476 m
1478 m
1483
1406
1488, 1479
1434, 1413
41
29 δ(CH)P + 24 ν(φ ) +
P
δ(CH)P +28ν(φ )+25ν(φ )
17 ν[φ (C N)]
I
P
I
1435 m
1442 w
1392 sh
ν10
1393 vs
39 δ(CH)P + 20 δ(NH)
18 ν(φ ) + 17 ν(φ )
30 δ(NHB)
+
+ 26 δ(CH)P + 21 δ(NHI)
P
I
+
15 ν[φ (C–N)]: in
I
plane-bending
δ(N–H· · ·N) HB vibration
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J. Raman Spectrosc. 2010, 41, 1021–1029

DFT quantum chemical calculations of 1H-imidazo[4,5-b]pyridine
Table 2. (Continued)
Experimental wavenumbers
Calculated wavenumbers
IPb
PED contributions
IPb
νn
IR
RS
Monomer
1367
Dimer
Monomer
Dimer
ν11
1386 m
1380, 1369
36
27 ν(φ ) + 19 ν(φ ) +
P
I
ν(φ )+23 ν(φ )+13 δ(NH)
15 ν(φ , φ ) + 17 δ(NHI)
P
I
P
I
+
13 δ(CH)P
ν12
ν13
1344 m
1315 s
1345 m
1315 s
1342
1314
1347, 1345
1316, 1314
24
27 ν(φ ) + 16 ν(φ ) +
P
I
ν(φ )+18 ν(φ )+16 δ(CH)I
13 δ(CH)I + 13 δ(CH)P
I
P
52
36 δ(CH)P + 33 ν(φ )
I
δ(CH)P +28ν(φ )+13ν(φ )
I
P
ν14
ν15
1278 m
1235 m
1279 s
1268
1239
1272
43 ν(φ ) + 32 ν(φ ) : [νas(ꢀ)]
33 ν(φ ) + 19 ν(φ ) : [νas(ꢀ)]
P
I
P
I
1236 m
1245, 1239
23 δ(CH)I + 19 δ(CH)P +
24 δ(CH)I + 17 ν[φ (C N)]
I
1
1
6 ν(φ ) + 12 ν(φ ) +
+ 20 ν(φ ) + 17 δ(CH)P +
P
I
P
2 δ(NH)
10 δ(NHI)
1
227 m
212 m
1226 m
1214 w
1193 w
1
ν16
ν17
1191 w
1167
1109
1172, 1169
1112, 1104
27 δ(φ ) + 24 ν(φ ) +
22 ν(φ ) + 20 δ(φ ) +
P
I
I
P
1
6 δ(CH)I + 16 δ(CH)P
14 δ(CH)I + 13 δ(CH)P
1119 w
1127 m
1117 m
1043 m
55 δ(CH)P + 29 ν(φ )
52 δ(CH)P + 18 ν(φ )
P
P
1115 m
ν18
ν19
1064
1029
1116, 1082
1030, 1028
59 ν[φ (C–N)I] + 29 δ(NH)
56 ν[φ (C–N)] + 28 δ(NHI)
I
I
+
13 δ(CH)I + 11 δ(NHB)
1036 w
1024 w
953 m
72 ν(φ ) + 20 δ(CH)P
72 ν(φ ) + 20 δ(CH)P
P
P
1023 vw
ν20
979 w
945
952, 936
79 γ (CH)P
79 γ (CH)P + 15 γ (φP)
972 w
954 m
ν21
ν22
ν23
ν24
ν25
934 w
899 m
890 w
912
910
875
844
778
925, 909
917, 903
879, 875
886, 849
784, 781
67 δ[φ (NCN)I] + 21 ν(φ , φ )
65 δ[φ (NCN)I] + 18 ν(φ , φ )
I
P
I
I
P
I
84 γ (CH)P
89 γ (CH)P
868 w
797 w
64 δ(φ ) + 28 ν(φ )
60 δ(φ ) + 19 ν(φ )
P
I
P
I
81 γ (CH)I + 13 γ (φ )
85 γ (CH)I + 14 γ (φ )
I
I
790 m
48 γ (φ ) + 30 γ (φ ) +
44 γ (φ ) + 30 γ (φ ) +
P
I
P
I
10 γ (CH)P
14 γ (CH)P
ν26
ν27
772
768
775, 768
771, 770
85 γ (CH)P
39 ν(φ ) + 28 ν(φ ) +
88 γ (CH)P
777 s
781 s
32 ν(φ ) + 14 ν(φ , φ ) +
P
I
P
P
I
1
4δ(φ )+10δ(φ ) : [νs(ꢀ)]
12 ν(φ )+12 δ(φ ) : [νs(ꢀ)]
I
P
I
I
7
95 w,vvb
748
73 γ (NHB): out-of-plane
γ (N–H· · ·N) HB vibration
ν28
641 w
643 m
632
632, 615
61 γ [φ (NCN)I]
55 γ [φ (NCN)I]
I
I
+
12 γ (CH)I + 12 γ (NH)
+ 21 γ (φ ) + 14 γ (NHI)
P
+
12 γ (CH)I
6
33 w
638 w
623 w
ν29
ν30
622 m
588 m
627
586
630, 627
584, 579
49 δ(φ ) + 29 δ(φ ) + 10 ν(φ )
41 δ(φ ) + 25 δ(φ ) + 16 ν(φ )
I
P
P
I
P
P
45 γ (φ ) + 28 γ (φ ) +
39 γ (φ ) + 38 γ (φ ) +
P
I
P
I
15 γ (CH)P
15 γ (CH)P
ν31
ν32
560 w
452 m
554 m
544
441
547, 545
74 δ(φ ) + 10 ν(φ )
74 δ(φ ) + 10 ν(φ )
P
I
P
I
461
79 γ (NHI) + 11 γ (φ )
I
460 vw
452, 442
53 δ(φ ) + 22 δ(φ )
51 δ(φ ) + 10 δ(φ )
P
I
P
I
455 vw
ν33
ν34
433 w
433
422
60 γ (NH) + 16γ (φ /φ )
P
I
426, 425
259, 252
57 γ (φ ) + 22 γ (NH): [γ (ꢀ),
68 γ (φ ) + 12 γ (φ /φ ) +
P
P
P
I
wagging]
10 γ (CH)P: [γ (ꢀ),
wagging]
ν35
ν36
274 w
250 w
285 vw
249
225
55 γ (φ ) + 27 γ (φ ) +
47 γ (φ ) + 23 γ (φ ) +
P
I
P
I
1
4 γ (φ /φ )
19 γ (φ /φ )
P
I
P
I
275 vw
251 w
229, 226
53 γ (φ /φ ) + 28 γ (φ ) +
51 γ (φ /φ ) + 27 γ (φ ) +
P
I
P
P
I
P
1
4 γ (φ ):
10 γ (φ ): [τ(ꢀ), wagging
I
I
of the whole molecule]
[
τ(ꢀ), wagging of the whole
molecule]
J. Raman Spectrosc. 2010, 41, 1021–1029
Copyright ꢀc 2009 John Wiley & Sons, Ltd.
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L. Dymi n´ ska et al.
Table 2. (Continued)
Experimental wavenumbers
Calculated wavenumbers
IPb
PED contributions
IPb
νn
IR
RS
Monomer
Dimer
Monomer
Dimer
1
52 w
15 w
90
67
93 ν(NHB)· · ·N
1
} Lattice vibration coupled
with ν(NH)· · ·N
72 γ (NHBN)
9
4 vw
51
93 δ(NHBN)
90 δ(NHBN)
100 γ (NHBN)
34
2
2, 15
φ , pyridine ring; φ , imidazole ring; ꢀ, φ + φ ; ν, stretching; δ, in-plane bending; γ , τ, out-of-plane bending; HB, hydrogen atom engaged in the HB;
P
I
P
I
HI, hydrogen atom of the imidazole ring (free for the dimer).
Figure 4. Raman spectra of IPb. Spectra a: experimental; spectra b: theo-
retical – calculated for the monomer; spectra c: theoretical – calculated for
the dimer.
−
1
as strong Raman band at 1279 cm and as medium intensity IR
−
1
band at 1278 cm
.
The second characteristic in-plane bending vibration of the IP
skeleton is described by the mode calculated for the monomer
−
1
−1
at 768 cm and for the dimer at 770 and 771 cm . It is a very
characteristic type of vibration in which the both rings breathe
simultaneously and therefore it is denoted as νs(ꢀ) symmetric
−
1
mode (Fig. 5). The νs(ꢀ) vibration is observed at 777 and 781 cm
in the IR and Raman spectra, respectively.
ThethirdunusualnormalmodeoftheIP skeletonisout-of-plane
vibration that can be identified as wagging motion of the whole
−
1
skeleton. The ν36 mode of the monomer, calculated at 225 cm
should be named as wagging vibrations because the P and I rings
behave as wings of a bird (Fig. 5).
Figure 3. IR spectra of IPb: (a) experimental; (b) theoretical – calculated for
the monomer; (c) theoretical – calculated for the dimer.
Temperature dependence of the IR and Raman spectra
in the considered wavenumber range correspond to the mixed
The IR and Raman spectra of IPb were measured at different
temperatures in the range 294–4 K starting from 294 K and
decreasing the temperature using the interval 5 K below 50
and 30 K in the range 50–293 K. The IR spectra in the ranges
δ(φ ) + δ(φ ) modes.
I
P
Amongthein-planestretchingmodes,theν14 mode(monomer)
and ν27–28 modes (dimer) that correspond to the asymmetric
νas(ꢀ) vibration of the whole skeleton have a special nature. In this
vibration both the rings breathe mutually, i.e. the enlargement
of one ring is associated with simultaneous shrinking of the
other ring (Fig. 5). The wavenumbers of these modes have been
−
1
2400–3400, 1000–1750, 760–880, and 50–180 cm are shown
in Figs 6 and 7. The temperature dependence of the Raman
spectrum is not shown because it is nearly not sensitive on the
temperature decrease. The Raman bands’ shift is very small and
−
1
−1
calculated at 1268–1272 cm and these vibrations are observed
do not exceed a few cm in the range 295–8 K.
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DFT quantum chemical calculations of 1H-imidazo[4,5-b]pyridine
Figure 5. Selected vibrational normal modes of the IP rings given in the vector form of the atomic displacements.
Analyzing the influence of the temperature lowering on the
position and shape of IR bands three different behaviors can be
seen. The majority of bands shift toward higher wavenumbers.
For instance, the wavenumber and full width at half maxima
vibrations of the NH· · ·N HB for the dimer are predicted by
1
−
the DFT calculations at the following wavenumbers: 3288 cm
−
1
−1
[ν(N –H· · ·N )]; 1413 and 1434 cm
[δ(N –H· · ·N )]; 748 cm
I
I
I
I
−
1
[γ (N –H· · ·N )];and90 cm {ν[(N H)· · ·N ]}. Thetheoreticalvalues
I
I
I
I
−
1
(
FWHM) of some bands in the region 900–1650 cm change
in the temperature range 294–4 K in the following way: 1622.3
5.3) → 1624.3 (3.4); 1475.6 (6.2) → 1475.9 (5.0); 1315.2 (5.8) →
316.4 (3.9); 1278.2 (7.5) → 1281.5 (5.6); 1115.0 (5.4) → 1117.0
agree well with the experimental data.
A broad contour is observed in the room temperature IR
−
1
(
1
spectrum in the range 2400–3400 cm having two maxima at
about 3100 and 2800 cm 1. This contour shifts into red with the
temperature decrease. Two components of this band correspond
to the asymmetric and symmetric vibrations of the NI –H· · ·NI
system.Thewavenumberandshapeofthestretchingν(NI –H· · ·NI)
band of IPb under study indicate that the intermolecular HB
between the nitrogen atoms of adjacent imidazole rings is
strong having similar properties as in the imidazole.
corresponding band observed in the range 2400–3400 cm
exhibits similar multiplet structure with numerous submaxima.
−
−
1
−1
(
2.6); 954.0 (5.7) → 957.3 cm (4.2 cm ). Such behavior for the
−
1
band at 1278 cm is illustrated in the inset of Fig. 6(b).
Vibrational characteristics and dynamics of the HB
[
31]
The NH group and imidazole nitrogen atoms of the adjacent
IPb molecules are involved in intermolecular HB. The formation
of the NI –H· · ·NI HB is postulated by the XRD data (Table 1).
These interactions strongly affect the IR spectra. The characteristic
The
−
1
[
31]
This structure was explained in terms of a Fermi resonance of
J. Raman Spectrosc. 2010, 41, 1021–1029
Copyright ꢀc 2009 John Wiley & Sons, Ltd.
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L. Dymi n´ ska et al.
Figure 6. Comparison of the IR spectra recorded at different temperatures
−
1
−1
at the range (a) 2400–3400 cm and (b) 1000–1750 cm . Inset shows
Figure 7. Comparison of the IR spectra recorded at different temperatures
−1
the temperature dependence of 1278 cm IR band.
−1
−1
in the range (a) 760–880 cm and (b) 50–180 cm . Inset in (a) shows
−
1
the temperature dependence of 790 cm IR band. Inset in (b) shows the
−1
temperature dependence of 152 and 115 cm IR band.
the ν(NH) fundamental with various combinations and overtones
of the internal vibrations. Another explanation was based on the
[
32,33]
frequency modulation theory
in which the subbands should
the temperature decrease. The clear and strong band observed
at 840 cm at 4 K appears at RT as a very broad absorption
−
1
obey a relationship νn = ν(AH) ± nν[(AH)· · ·B] where n = 0.1.2
[
34]
−1
and ν[(AH)· · ·B] is any HB frequency. The temperature behavior
of the observed subbands suggests that the former explanation is
proper. The temperature decrease causes the shift of the majority
of these submaxima toward the higher wavenumber and increase
of its intensity. When going from 294 to 4 K the shift is insignificant
expanded from 760 to 820 cm giving rise to increased base line
−
1
of the IR spectrum. Its FWHM at RT is 99 cm . At 200 K it appears
as a well-shaped band that strongly narrows to 40 cm with the
temperature decrease (see Fig. 7(a)). At 4 K the FWHM of this band
−
1
−
1
equals 12.7 cm . Such behavior allows us to assign this band to
−
1
−1
for the bands at 3000–3200 cm (ꢁν ≈ 0.2–2.0 cm ) and
the out-of-plane γ (NI –H· · ·NI) vibration.
−
1
−1
−1
significant in the range 2500–3000 cm
(4–10 cm ). For
Very similar behavior is observed for the IR band at 152 cm
−
1
−1
−1
example, the bands at 2773, 2811.5, 2855, and 2981 cm shift
to 2779, 2817.3, 2861, and 2984 cm , respectively. The line at
(FWHM = 10.3 cm ) at 294 K, which shifts to 165 cm at 4 K
−
1
−1
(FWHM = 8.0 cm ) (see inset Fig. 7(b)). This band is assigned
−
1
−1
2
923 cm shows opposite shift to 2917 cm . The components
to the stretching ν[(NH)· · ·N] vibration of the H· · ·N bond which
−
1
in the range 2800–3150 cm correspond to the ν(CH) internal
vibrations of the IP system.
according to the results of quantum chemical calculations is
−
1
expected near 100 cm . The shape of all these broad contours is
typical for those observed for other HB systems.[
35–40]
The in-plane bending vibration of the NI –H· · ·NI HB appears at
room temperature as a clear rising of the spectral base line in the
It is well known that the effect of the temperature increasing
on phonon energy is mainly due to the thermal expansion of
−
1
IR spectrum in the range 1200–1350 cm . This contour changes
slightly with the temperature because it is masked by the strong
bands of the IPb vibrations.
Two IR contours observed at 760–850 and 150–170 cm show
exceptionalbehaviorasafunctionoftemperature(seeFig. 7(a)and
the lattice.[
35–39]
The Cui formula
[38,39]
is often employed to
interpret the changes in Raman spectra, i.e. the temperature
−
1
Bꢀω /k T
−1
,
0
B
dependence of Raman bands is ω(T) = ω0 − A(e
− 1)
where ω0 is the Raman phonon wavenumber at 0 K, kB is
Boltzman constant, and A and B are fitting parameters. Other
(
b)). Their intensity strongly increases and FWHM decreases with
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Copyright ꢀc 2009 John Wiley & Sons, Ltd.
J. Raman Spectrosc. 2010, 41, 1021–1029

DFT quantum chemical calculations of 1H-imidazo[4,5-b]pyridine
approach is used when the two-level Schottky model is applied.[40]
In this approximation the peak wavenumber and HWHM are
[5] G. Cristalli, S. Vittori, A. Eleuteri, M. Grifantini, R. Volpini, G. Lupidi,
L. Capolongo, E. Pesenti, J. Med. Chem. 1991, 34, 2226.
[6] A. M. Bergman, G. Cristalli, S. Vittori, J. Wang, S. Eriksson, G. J. Peters,
Nucleosides Nucleotides 1999, 18, 897.
−
1
reproducedbythefollowingfunctionsoftemperature: ν(T)[cm
a+b exp(−c/T)/1−exp (−c/T), where a is the wavenumber at
K, b is the amplitude of the temperature dependent term, and c
]
=
[
7] M. Kimoto, K. Moriyama, S. Yokoyama, I. Hirao, Bioorg. Med. Chem.
Lett. 2007, 17, 5582.
0
is the characteristic temperature of the temperature dependence.
The application of this relationship for the IR bands observed at
about 795, 152, and 120 cm gives the plots shown in Fig. 7. The
best fit to the experimental data leads to the following values of
[8] R. F. Service, Science 2000, 289, 232.
9] J. Lorenc, Z. Talik,
L. Dymi n´ ska,
A. Waokowska, L. Macalik, J. Raman Spectrosc. 2008, 39, 1.
10] C. Lee, W. Yang, R. G. Parr, Phys. Rev. B 1988, 41, 785.
11] D. Becke, J. Chem. Phys. 1993, 98, 5648.
[12] R. G. Parr,W. Yang, Density-functionalTheoryofAtomsandMolecules,
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[
J. Hanuza,
M. M1czka,
−
1
[
[
−
1
−1
a = 839, 164, and 122.4 cm ; b = −130, −7, and −3.8 cm , and
−
1
c = 445, 125, and 124 K for the bands at 795, 152, and 120 cm
,
[
[
[
respectively. These values are close to reported ones for other
HB systems.[ Negative values of b parameter, corresponding to
the decreasing wavenumber with increasing temperature, are a
common behavior observed for weakly anharmonic vibrations.[
Finally, itshouldbenotedthatinthepresentworkthepossibility
of the NI –H· · ·NP HB bond formation between the inidazole NI –H
bond and pyridine NP atom was also considered. The calculated
wavenumbers for such HB coupled dimer are nearly the same
40]
[16] P. C. Hariharan, J. A. Pople, Mol. Phys. 1974, 27, 209.
[17] M. S. Gordon, Chem. Phys. Lett. 1980, 76, 163.
40]
[
[
[
18] R. C. Binning Jr, L. A. Curtis, J. Comput. Chem. 1990, 11, 1206.
19] M. J. Frish, J. A. People, J. S. Binkley, J. Chem Phys. 1984, 80, 3265.
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J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery Jr, R. E.
Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels,
K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi,
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−
1
(
the difference is 1–2 cm ) and they have nearly the same PED
contributions. The exceptional behavior is observed for the bands
−
1
calculated at 3288, 1082, and 748 cm for the NI· · ·NI dimer that
shift to 3264, 1073, and 757 cm for the NI· · ·NP dimmer, i.e. their
ν differences are 24, 10, and 9 cm , respectively.
−
1
1
1
ꢁ
Conclusions
[
[
The following conclusions can be drawn from the XRD studies,
vibrational measurements, and DFT calculations performed in the
present work:
22] M. A. Palafox, V. K. Rostogi, Spectrochim. Acta, Part A 2002, 58, 411.
[23] D. Michalska, RAINT (Raman Intensities), a Computer Program for
CalculationofRamanIntensitiesfromtheGaussianOutputs, Wroc3aw
University of Technology: Wroc3aw, 2002.
1
2
3
.
.
.
The structural parameters derived from the DFT optimization
approximate the experimental XRD data well. They are also
in good agreement with similar compounds described in
literature.
Vibrational properties of the IPb obtained in the present work
using a new synthesis procedure are identical to those of the
commercially available materials. The method proposed by us
allows to obtain single crystals suitable for XRD studies.
Vibrational characteristics of the imidazopyridine double
system exhibit several characteristic modes that remain nearly
unchangedforthecompoundscontainingthisskeleton. These
vibrations could be used as the diagnostic tool for other
systems containing the IPb unit.
The structures of the compounds studied are stabilized by the
HBs between the proton of the imidazole ring (NH bond) and
imidazole nitrogen of the adjacent molecule. The properties of
the NI –H· · ·NI HB have been analyzed using the temperature
dependence of the respective bands and Schottky’s two-level
model. The results of the low temperature IR and Raman
studies allow us to characterize the properties of the HB in the
IPb system.
[24] D. Michalska, R. Wysoki n´ ski, Chem. Phys. Lett. 2005, 403, 211, and
references cited therein.
[
25] M. M. Szcz e¸ s´ oniak, B. Maolanka, AniMol computer program: infrared
and Raman spectroscopy teaching and research tool, version 3.21,
1
995–1997.
[26] H. Rostkowska, L Łapi n´ skiM. J. Nowak, Vibr. Spectr. 2009, 49, 43 (M.
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[
27] Oxford Diffraction, CrysAlisCCD and CrysAlisRED, Including ABSPACK.
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28] G. M. Sheldrick, Acta Crystallogr., Sect. A 2008, 64, 112.
29] CCDC 742833 contains the supplementary crystallographic
data for this paper. These data can be obtained free of
charge via www.ccdc.cam.ac.uk\data request\cif, or by emailing
data request@ccdc.cam.ac.uk, or by contacting The Cambridge
Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ,
UK; fax: +44 12 23 336033.
[
[
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[
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[
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Copyright ꢀc 2009 John Wiley & Sons, Ltd.
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