Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 127 (2014) 4146

Contents lists available at ScienceDirect

Spectrochimica Acta Part A: Molecular and

Biomolecular Spectroscopy
journal homepage: www.elsevier.com/locate/saa

Effect of intermolecular hydrogen bonding, vibrational analysis

and molecular structure of a biomolecule: 5-Hydroxymethyluracil
agr rak a,, Yusuf Sert b,d, Fatih Ucun c
a

Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan, Turkey
Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat, Turkey
c
Department of Physics, Faculty of Art & Sciences, Sleyman Demirel University, Isparta, Turkey
d
Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey
b

h i g h l i g h t s

g r a p h i c a l a b s t r a c t

 The FT-IR spectra of 5-

hydroxymethyluracil is recorded in
solid phase.
 Theoretical vibrational modes and
molecular structure are given for the
rst time.
 The dimeric form of 5hydroxymethyluracil is simulated.
 Effect of intermolecular hydrogen
bonding to vibrational modes are
discussed.

a r t i c l e

i n f o

Article history:
Received 26 September 2013
Received in revised form 26 January 2014
Accepted 9 February 2014
Available online 22 February 2014
Keywords:
5-Hydroxymethyluracil
5hmU
FT-IR
Hydrogen bonding
M06-2X
B3LYP

a b s t r a c t
In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were
investigated. The FT-IR (4000400 cm 1) spectrum of the molecule in the solid phase was recorded. The
geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the
title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods
with the 6-311++G(d,p) basis set for the rst time. The optimized geometric parameters and theoretical
vibrational frequencies were found to be in good agreement with the corresponding experimental data,
and with the results found in the literature. The vibrational frequencies were assigned based on the
potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil
molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational
frequencies. It was observed that the NAH stretching modes shifted to lower frequencies, while its inplane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NAH


O
hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular
orbital (LUMO) energies and diagrams were presented.
2014 Elsevier B.V. All rights reserved.

Introduction
Recent spectroscopic studies of uracil and its derivatives have
been motivated on their biological and pharmaceutical properties.
Corresponding author. Tel.: +90 446 224 3032/40042.
E-mail address: ccirak@erzincan.edu.tr (. rak).
http://dx.doi.org/10.1016/j.saa.2014.02.017
1386-1425/ 2014 Elsevier B.V. All rights reserved.

Uracil and its derivatives belong to the heterocyclic group.

N-heterocyclic molecules such as pyrimidine, cytosine, uracil and
their derivatives have immense importance since some of them
are the basic constituents of DNA and RNA, and play an important
role in constitution properties of nucleic acids. Because of their
biological activities, pyridine-derived biomolecules have received

42

. rak et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 127 (2014) 4146

much attention from spectroscopic, clinical, drug, and industrial

researchers [19].
5-Hydroxymethyl-uracil (5hmU) is a product of oxidative attack
on the methyl group of thymine in DNA. Hydroxy radical may
cause different modication of DNA bases. Intermolecular hydrogen bonding is a key to the formation of crystal structure of matter.
However, the hydrogen bonding causes signicant shifts in vibrational frequencies of some characteristic modes, so the vibrational
spectroscopy is very important tool for understanding the effect of
the hydrogen bonding. Qiu et al. have presented the hydrogen
bonding complexes formation involving hmU bound to the four
bases in DNA [10]. Also, the dynamics of the hydrogen bonding
in an excited state are very different. Indeed, the hydrogen bonding
in excited states is particularly important in photophysical
processes and photochemical reactions. Excited-state hydrogenbonding dynamics are mainly determined by vibrations of hydrogen donor and acceptor groups [11]. Zhao and Han have made
signicant contributions to the literature regarding the effect of
hydrogen bonding on vibrational spectra in an excited state
[12,13], internal conversion and intersystem crossing [14,15], and
intramolecular charge transfer in an excited state [16].
To our best knowledge, no computational vibrational study on
the monomeric and dimeric structure of 5hmU has been published
in the literature. Hence, in the work described in this paper The
theoretical and experimental study were performed to obtain a detailed description of the molecular structure and vibrational spectra of 5hmU, utilizing M06-2X and density functional theory (DFT/
B3LYP) methods with the 6-311++G(d,p) basis set. The experimental FT-IR spectrum of the molecule was recorded and compared
with the results of the theoretical data. In addition, the shifts in
the vibrational frequencies relative to the dimeric 5hmU were
determined in order to investigate the effects of intermolecular
hydrogen bonding in the ground state.
Experimental details
5hmU was purchased from SigmaAldrich (St. Louis, MO, USA)
and, used (i.e., its spectra were recorded) with no further purication. The FT-IR spectrum (4004000 cm 1) of a KBr disk of 5hmU
was recorded using a Perkin Elmer (Waltham, MA, USA) Spectrum
One FT-IR spectrometer with a resolution of 4 cm 1 at room temperature. Also, the Raman spectrum of 5hmU was recorded using
different spectrophotometers with different laser sources. But,
uorescence cannot be eliminated in the Raman spectrum. So, recorded Raman spectrum was not considered for this study.

has 16 atoms. Three Cartesian displacements of 16 atoms provide

48 internal and 42 normal vibration modes. The total energies (corrected for the zero point energy) for the molecule, calculated using
M06-2X and B3LYP with the 6-311++G(d,p) basis set, are given in
Table 1. As clearly seen form the table, the geometry optimized
using the B3LYP level of theory has lower energy.
Geometry
The chemical formula of 5hmU is C5H6N2O3. Its optimized geometric parameters (bond lengths and bond angles) obtained using
M06-2X and B3LYP methods with the 6-311++G(d,p) basis set are
presented in Table 2. In the Table 2 are also given the experimental
geometric parameters for comparative purpose [25]. As seen from
this comparison, the optimized geometric parameters of 5hmU are
in good agreement with the experimental data. The slight differences observed between the calculated and experimental values
result from the fact that the theoretical calculations were performed for the isolated 5hmU in the gaseous phase, while the
experimental results were obtained for the solid phase of
the 5hmU. In addition, the comparison of the theoretical bond
lengths and bond angles at the M06-2X and B3LYP levels as a
whole shows that the calculated values at the B3LYP level correlate
well with the experimental ones. The largest differences between
the calculated (DFT/B3LYP) and experimental geometric parameters are: 0.047 for the N1AC1 bond length, 0.023 for N1AC5,
0.16 for C1AO1, 0.054 for C1AN2, 0.025 for N2AC2, 0.044
for C2AO3 , 0.024 for O2AH2, 0.015 for C4AH3, 0.021 for
C4AH4, 0.061 for C3AC4. 3.3 for the bond angle C1AN1AC5,
2.7 for N1AC1AO1, 4.5 for C5AN1AH5, 4.1 for O1AC1AN2,
6.1 for N2AC2AC3, 10.1 for O3AC2AC3, 7.9 for C2AC3AC4
and 6.3 for H3AC4AH4. The calculated bond lengths and angles
of the uracil group are also in good agreement with those given
in [26,27]. Rasheed et al. [26] have calculated the C@O bond length
as 1.2171.220 , NAH as 1.0101.014 , NAC as 1.3751.414 ,
and CAC as 1.3501.461 . These values have been determined
experimental as 1.2451.215 for the C@O bond length, 0.84
0.88 for NAH, 1.3711.430 for NAC and 1.3401.430 for
CAC [27]. As seen from these experimental bond lengths, the calculated DA (Donor and Acceptor) values show very good agreement
with the recorded spectral data, since in our molecule there are
intermolecular hydrogen bonding interactions between NAH


O
atoms. Fig. S1 (Supplementary information) shows the optimized

Computational details
The optimized structure parameters, harmonic vibrational frequencies, IR intensities and Raman scattering activities of 5hmU
were calculated using M06-2X and DFT/B3LYP methods with the
6-311++G(d,p) basis set. All the computations were performed
using the Gaussian 09 program package [17]. The calculated harmonic frequencies were scaled by 0.9489 and 0.9614 for the
M06-2X and B3LYP levels of theory with the 6-311++G(d,p) basis
set [18,19], respectively. Additionally, the calculated vibrational
frequencies were claried by performing a potential energy distribution (PED) analysis of all the fundamental vibration modes using
the VEDA 4 program [20]. The VEDA 4 has been used in previous
studies by many researchers to realize PED analysis of vibrational
modes [2124].
Results and discussion
The optimized molecular structure of 5hmU is shown in Fig. 1
along with the atom numbering scheme. 5hmU is a molecule that

Fig. 1. The optimized molecular structure of the 5hmU.

. rak et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 127 (2014) 4146

43

Table 1
Sum of electronic and zero point energies (hartree/particle), dipole moments (debye), HOMO (a.u), LUMO (a.u) and HOMOLUMO gap values of 5hmU.
Methods

6-311++G(d,p)
Energies

M06-2X
B3LYP

Dipole moment

529.30871539
529.51504509

HOMO energies

3.7640
3.7995

0.31886
0.26923

Table 2
Experimental and calculated geometric parameters of 5hmU with 6-311++G(d,p).
Geometric parameters

Bond lengths ()
N1AC1
N1AC5
N1AH5
C1AO1
C1AN2
N2AC2
N2AH1
C2AO3
C2AC3
O2AH2
O2AC4
H3AC4
H4AC4
C3AC4
C3AC5
C5AH6
R2
Bond angles ()
C1AN1AC5
C1AN1AH5
N1AC1AO1
N1AC1AN2
C5AN1AH5
N1AC5AC3
N1AC5AH6
O1AC1AN2
C1AN2AC2
C1AN2AH1
C2AN2AH1
N2AC2AO3
N2AC2AC3
O3AC2AC3
C2AC3AC4
C2AC3AC5
H2AO2AC4
O2AC4AH3
O2AC4AH4
O2AC4AC3
H3AC4AH4
H3AC4AC3
H4AC4AC3
C4AC3AC5
C3AC5AH6
R2

Calculated values

Experimental values

M06-2X

Ref. [1]

B3LYP

1.384
1.375
1.009
1.204
1.383
1.394
1.013
1.214
1.463
0.964
1.410
1.096
1.091
1.503
1.342
1.083
0.9539

1.390
1.377
1.009
1.212
1.387
1.401
1.013
1.222
1.462
0.966
1.422
1.098
1.092
1.507
1.349
1.084
0.9554

123.8
115.0
123.3
112.3
121.2
122.4
115.4
123.8
127.6
115.6
116.8
120.9
115.0
124.2
116.7
118.4
106.9
110.5
107.0
112.1
108.1
109.2
109.8
124.9
122.3
0.8445

123.8
115.2
123.2
112.7
121.0
122.4
115.2
124.0
127.7
115.7
116.6
120.6
114.9
124.5
117.4
118.4
106.8
110.3
106.6
112.7
107.8
109.3
110.0
124.2
122.4
0.8763

1.437
1.400
1.012
1.372
1.441
1.426
1.012
1.266
1.502
0.942
1.392
1.113
1.113
1.568
1.429
1.100

127.1
116.5
120.5
111.4
116.5
121.9
119.1
128.1
124.7
117.6
117.6
124.5
121.0
114.4
125.3
113.9
106.9
107.8
105.7
115.9
114.1
107.8
105.7
120.8
119.1

geometry of the dimeric 5hmU. However, there can be seen small

differences between the calculated and experimental hydrogenbond distances H


O because the calculated NAH bonds are larger
than the experimental ones.
Additionally, to determine the exact orientation of the hydroxymethyl group, we have employed dihedral driver using ChemBio3D
Ultra 12.0 software for the C3AC4AO2AH2 dihedral angle in interval 1 [28]. Also, this optimized structure has been used to obtain
input le for the calculations.
Vibrational assignments
The experimental FT-IR spectrum of 5hmU is shown in Fig. 2.
For comparative purposes its calculated IR spectrum is shown in

LUMO energies
0.02726
0.06847

HOMOLUMO gap value energies

0.29160
0.20076

Fig. 3. The scaled harmonic vibrational frequencies at the M062X and B3LYP levels of theory as well as the observed vibrational
frequencies are presented in Table 3. The scaling procedure was
performed to improve the agreement between the harmonic and
observed vibrational frequencies [29]. Table 3 also includes the
detailed PED assignments and the calculated IR intensities. As we
stated before the 5hmU molecules are interconnected by NAH


O
hydrogen bonds in the solid phase, so the observed and calculated
frequencies of the monomeric 5hmU do not agree for some modes.
Thus, in order to determine the shifts in the normal modes due to
the effect of intermolecular hydrogen bonding, we have calculated
the vibrational frequencies of the dimeric 5hmU using the B3LYP
level of theory with the same set and given them in Table 4. From
the comparison of Tables 3 and 4, we can state that the calculated
frequencies for the vibrational modes of the monomeric 5hmU are
strongly affected by the intermolecular hydrogen bonding. The
modes consisting of the lower frequency shifts than 5 cm 1 were
not shown in Table 4.

CAC vibrations
The bands between 1400 and 1650 cm 1 in benzene derivatives
are assigned to CAC stretching modes [30]. Accordingly in the
present study, the CAC vibrations are observed at 1630 cm 1 in
the FT-IR spectrum of 5hmU. As theoretically these vibrations have
been calculated 1648 and 1624 cm 1 by using M06-2X and B3LYP
methods, respectively, and PED value of 64% has been reported
(Table 3). These vibrations were observed at 1468 cm 1 in FT-IR
spectrum of 5,6-diamino uracil and 1440 cm 1 in its FT-Raman
spectrum, and at 1422, 1495 cm 1 in the FT-IR spectrum of 5,6dihydro-5-methyl uracil and 1493, 1567 cm 1 in its FT-Raman
spectrum [31].

CAN vibrations
The identication of CAN stretching frequency is a very difcult
task since the mixing of bands are possible in this region [31].
Hence in this region the FT-IR bands are observed at 1358, 1154,
1122 and 1048 cm 1 in the spectrum of 5hmU. Their assignments
were made in accordance with the those proposed by Singh [32].
These bands have been observed at 1364, 1371, 1432, 1532 cm 1
in the FT-IR spectrum of 5,6-diamino uracil and at 1392, 1533,
1639 cm 1 in its Raman spectrum [31].

CAH vibrations
In the heterocyclic organic molecules, CAH stretching modes
are observed commonly in the region 31003000 cm 1 [29]. The
CAH stretching mode is calculated at 3070 cm 1 in B3LYP method
(Table 3). From the experimental FT-IR spectrum of 5hmU given in
Fig. 2, the observed peak at 3070 cm 1 is attributed to the CAH
stretching mode. As seen from the PED analysis in the Table 3,
the CAH in plane bending vibrations (dHCC) contributes to some
frequencies in the region 11491624 cm 1. Hence, the FT-IR bands
at 1630, 1301 and 1122 cm 1 are assigned to the CAH in plane
bending modes. sHCCC mode has been assigned to the band at
938 cm 1 in the FT-IR spectrum of the molecule.

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. rak et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 127 (2014) 4146

Fig. 2. The experimental FT-IR spectrum of 5hmU in solid phase.

764 (IR) cm
mode.

Fig. 3. Graph of the calculated IR spectra.

C@O vibrations
The typical characteristic absorption bands of the C@O stretching vibrations of uracil and its derivatives are very complex, and
appear as very broad and strong IR bands [33]. At rst glance,
the observed band at 1744 cm 1 (IR) and 1701 cm 1 (IR) can be assigned to the C2@O3 and C1@O1 stretching modes, respectively.
But, the C2@O3 stretching frequency is calculated at lower value
than the C1@O1 mode for the dimeric 5hmU. The crystal structure
consists of 5hmU molecule linked by dimeric NAH


O hydrogen
bonds involving N1, N2 and the keto oxygen O1 [34]. The oxygens
O2 and O3 are not a part of this NAH


O hydrogen bond. As seen
from the Table 4, the C1@O1 stretching mode frequency changes
noticeably due to the hydrogen bonding. The frequency calculated
at 1671 cm 1 for the monomeric 5hmU (Table 3) is shifted by
25 cm 1 to the higher frequency of 1705 cm 1 for the dimeric
5hmU (Table 4), while C2@O3 stretching mode frequency is calculated at 1735 and 1734 cm 1 for the monomeric and dimeric
5hmU, respectively. For this reason, we think that the observed
bands at 1701 (IR) cm 1 should be assigned to the C2@O3 and
C1@O1 stretching modes. Furthermore, the observed bands at

can be assigned to the C@O out of plane bending

NAH vibrations
In the heterocyclic molecules, the NAH stretching vibrations are
observed in the region 35003000 cm 1 [35]. As seen from Table 3,
the two NAH stretching modes are calculated to be 3494 and
3454 cm 1. These frequencies are observed at 3496 and
3396 cm 1 in the FT-IR spectrum of 5hmU, respectively. Ten
et al. have observed these modes at 3479 and 3432 cm 1 for isolated thymine [36]. As shown from Table 4, the calculated
N1AH5 and N2AH1 stretching modes are shifted by 300 cm 1 to
3187 and 3148 cm 1 for the dimeric 5hmU, respectively. Palafox
et al. have calculated NAH stretching modes at 3184 and
3151 cm 1 for dimeric 5-aminouracil [37]. These shifted NAH
stretching modes are assigned to the modes at 3496 (IR) and
3396 (IR) cm 1, respectively.
As seen from PED analysis in Table 3, the NAH in plane bending
(dHNC) vibrations contribute to the calculated four frequencies at
1735, 1442, 1355 and 1149 cm 1. These frequencies were assigned
to the bands at 1740, 1465, 1341 and 1122 cm 1 in IR spectrum
(Fig. 2). As seen from the Table 4, the NAH in plane bending mode
is shifted by 40 cm 1 to the higher frequencies due to the hydrogen
bonding effect in the dimeric 5hmU. This shifted frequency is calculated at 1188 cm 1, and assigned to the mode 1122 (IR) cm 1.
The computed NAH in plane bending frequencies in Tables 3 and
4 show excellent agreements with the recorded spectra and literature [3639].

OAH vibrations
Bands due to OH stretching are of medium to strong intensity in
IR spectra although it may be broad. Unassociated hydroxyl groups
absorb strongly in the region 36703580 cm 1. The calculated
band due to the free hydroxyl group is sharp and, its intensity increases. For solids, liquids and concentrated solutions a broad band
of less intensity is normally observed [4042]. The OAH stretching
mode was calculated at 3632 cm 1 (Table 3). From the experimental FT-IR spectrum given in Fig. 2, the observed peak at 3637 cm 1
was assigned to the OAH stretching mode.

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. rak et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 127 (2014) 4146
Table 3
Observed and calculated vibrational frequencies of 5hmU with 6-311++G(d,p).
Vibration No.

Calculated frequencies in cm

m1
m2
m3
m4
m5
m6
m7
m8
m9
m10
m11
m12
m13
m14
m15
m16
m17
m18
m19
m20
m21
m22
m23
m24
m25
m26
m27
m28
m29
m30
m31
m32
m33
m34
m35
m36
m37
m38
m39
m40
m41
m42
R2

(IR intensities)

Observed frequencies

M06-2X

B3LYP

FT-IR

3658 (73.5)
3480 (136.0)
3432 (92.1)
3058 (1.4)
2964 (15.6)
2896 (32.3)
1765 (841.5)
1710 (761.2)
1648 (68.7)
1448 (184.8)
1425 (3.2)
1372 (96.0)
1364 (76.2)
1349 (3.7)
1319 (13.2)
1315 (9.2)
1187 (1.0)
1169 (23.1)
1155 (145.0)
1097 (2.0)
1053 (134.7)
950 (31.3)
928 (14.0)
892 (9.2)
789 (11.9)
741 (8.8)
728 (53.3)
711 (2.1)
638 (86.0)
586 (3.9)
543 (68.4)
531 (30.7)
514 (152.3)
493 (29.3)
394 (15.7)
380 (22.4)
359 (14.4)
267 (4.6)
193 (0.8)
148 (2.0)
120 (4.3)
80 (1.7)
0.9992

3632 (58.0)
494 (108.9)
3454 (71.5)
3070 (2.9)
2967 (21.7)
2886 (41.8)
1735 (815.8)
1671 (655.8)
1624 (38.7)
1442 (102.5)
1434 (2.7)
1373 (41.9)
1362 (143.3)
1355 (8.9)
1323 (19.5)
1316 (6.6)
1181 (17.2)
1168 (76.2)
1149 (78.3)
1093 (8.6)
1007 (113.2)
951 (40.1)
925 (13.7)
883 (10.6)
790 (12.5)
745 (14.1)
726 (44.6
708 (1.8)
649 (77.9)
586 (4.2)
548 (71.4)
535 (17.8)
510 (96.8)
480 (83.3)
394 (13.4)
379 (21.5)
359 (13.4)
267 (4.7)
183 (0.4)
147 (1.7)
99 (5.5)
75 (3.7)
0.9994

3637
3496
3396
3070
2991
2876
1740
1701
1630
1465
1432
1421
1358
1341
1341
1301

Assignments

tOH(100)
tNH(99)
tNH(99)
tCH(99)
tCH(99)
tCH(99)
tOC(75)+dHNC(11)
tOC(73)
tCC(64)+dHCC(12)
dHNC(43)+tNC(23)+dCCN(12)
dHCH(92)
dHCO(36)+dHOC(15)+sHCCC(12)
tCN(23)+dHOC(13)+dHCO(12)+dOCN(10)
dHNC(67)+tOC(12)
dHOC(25)+sHCOH(21)+sHOCC(1O)
dHCC(28)+sHCOH(25)
tCC(23)+tCN(12)+dHCC(12)+dHCO(12)
tCN(24)+dHOC(13)+sHCOH(11)
tCN(43)+dHNC(19)+dHCC(13)
tCN(31)
tOC(84)
dCNC(13)+sHCCC(13)+tCN(11)+sOCCC(10)
sHCCC(14)+dCNC(13)
sHCCC(71)
dCCN(15)+tCC(12)+dOCC(10)
cONNC(54)+tCN(11)
cONNC(94)
tCN(26)+dNCN(23)+dCNC(11)
sHNCN(87)
dOCN(42)+dNCN(14)
sHNCN(68)
sHNCN(24)+dCNC(14)+dOCC(10)
dOCN(23)+dCNC(17)+dOCC(12)+sHOCC(11)
sHOCC(62)
cCCCC(12)+dNCN(12)+dCNC(11)
dONC(47)+sCCNC(16)+tCN(12)
sCCNC(27)+dOCN(13)
dCCC(45)+sHCCC(14)+cCCCC(11)
dOCC(24)+cCCCC(22)+dCCC(19)+ sNCNC(10)
sNCNC(84)
sNCNC(39)+sOCCC(24)+sCCNC(18)
sNCNC(35)+cCCCC(24)+sCCNC(15)+ cOCCC(12)

1154
1122
1048
1013
938
916
829
802
764
748
660
560
560
530
455
429

m: stretching, d: bending, c: out of plane bending, s: torsion.

Potential energy distribution (PED) values lower than 10% are neglected.

Table 4
Observed and calculated vibrational frequencies of 5hmU calculated at the B3LYP/6-311++G(d,p) level of theory.
Vibration No.

m2
m3
m8
m13
m19
m29
m32
m35
m39

Calculated frequencies in cm

(IR intensity)

Monomeric

Dimeric

3494 (108.9)
3454 (71.5)
1671 (655.8)
1362 (143.3)
1149 (78.3)
649 (77.9)
535 (17.8)
394 (13.4)
183 (0.4)

3187 (2447.8)
3148 (162.7)
1705 (1314.6)
1396 (125.6)
1188 (79.4)
591 (0.5)
514 (56.8)
407 (217.0)
108 (5.6)
65 (0.7)
51 (2.3)

Energies, dipole moments and molecular orbital energies

The sum of electronic and zero point energies, the dipole moments, HOMO and LUMO and HOMOLUMO gap energy values of
the molecule at M06-2X and B3LYP/6-311++G(d,p) level have been
calculated. According to the theoretical results the molecule is

Shift values (cm

Observed frequencies

Mode assignments

FT-IR
307
306
25
34
39
58
21
13
75

3496
3396
1701
1358
1122
660
530
429

m(NAH)
m(NAH)
m(OAC)
m(NAC)
d(NAH)
s(HNCN)
d(CAO)
d(NAC)
d(OCC)
Lattice mode
Lattice mode

more stable at B3LYP/6-311++G(d,p) level. The prediction of accurate dipole moments is very important issue because the magnitude of dipole moment is strongly related to structural stability.
If the structural stability is high, dipole moment is lower. For our
molecule the structural stability at B3LYP/6-311++G(d,p) level is
high since the dipole moment is lower than one at M06-2X.

46

. rak et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 127 (2014) 4146

The frontier molecular orbital plays an important role in electric

and optical properties of molecules as well as in UVvis and chemical spectra [4345]. The highest occupied molecular orbital
(HOMO) energies, the lowest unoccupied molecular orbital
(LUMO) energies, and the gap energy value of HOMOLUMO for
5hmU are calculated at the M06-2X and B3LYP/6-311++G(d,p) level of theory, and are shown in Table 1. As a result, at M06-2X/6311++G(d,p) level, the HOMOLUMO gap value is higher than the
one at B3LYP/6-311++G(d,p) level. The LUMO as an electron acceptor represents the ability to obtain an electron and the HOMO represents the ability to donate an electron. HOMOLUMO plot at
B3LYP/6-311++G(d,p) level is given in Fig. S2 (Supplementary
information). As seen from the gure, the HOMO is located on
the hydroxymethyl group, C@O groups and NAC group, partially
over the ring, the LUMO is more focused over the ring.
Conclusion
In this work, we have performed the experimental and theoretical vibrational analysis, and investigated the structural geometry
of 5-hydroxymethyl-uracil. The calculations have been performed
at the M06-2X and B3LYP levels of theory with the 6311++G(d,p) basis set. Based on the calculated energies, the optimized structure at the B3LYP/6-311++G(d,p) level of theory has
lower energy. The parameters of the optimized structure were seen
to be in good agreement with the results of the experimental data.
The scaled harmonic vibrational frequencies were compared with
those observed in the recorded FT-IR spectrum of the molecule,
and seen quite good agreement. Also, the results of our detailed
PED analysis were seen to be good agreement with the results reported in the literature and theoretical background. The vibrational
analysis of the molecule enabled us to evaluate the effect of the
hydrogen bonding and to improve the accuracy of assignments in
the experimental spectra. The calculations performed at the
B3LYP/6-311++G(d,p) level have yielded good results for the molecule in the terms of the calculated frequencies and optimized geometric parameters than those at the M06-2X/6-311++G(d,p) level.
The HOMO and LUMO and gap energies of the molecule were also
given.
Appendix A. Supplementary material
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.saa.2014.02.017.
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