Download Density functional theory and FTIR spectroscopic study of carboxyl

Indian Journal of Pure & Applied Physics
Vol. 43, December 2005, pp. 911-917
Density functional theory and FTIR spectroscopic study of carboxyl group
Medhat Ibrahim1, Abdallah Nada2, & Diaa Eldin Kamal1
1
Spectroscopy Department, National Research Center, Dokki, Cairo, Egypt
Cellulose and Paper Department, National Research Center, Dokki, Cairo, Egypt
2
Received 29 March 2005;revised 7 September 2005;accepted 30 September 2005
Both molecular modelling and FTIR have been used to study carboxyl group among acetic acid, potassium and sodium
acetate, glycine, sodium salicylate, salicylic acid and cellulose acetate. Molecular modelling was used to study formic acid,
carboxylic acids R-COOH, monovalent alkali carboxylate CH3COO-M, alanine, benzoic acid as well as naphthalene. Each
structure was optimized using VWN/DZVP then vibrational spectra were further calculated at the same level of theory. The
comparison between both calculated and experimental spectra showed good agreement with each other. Except for formic
acid and free carboxyl, the characteristic band is shifted towards lower frequency.
Keywords: FTIR spectroscopy, Density functional theory, Carboxyl group, Cellulose acetate
IPC Code: G01J3/28
1 Introduction
Studying carboxyl group (COOH) and its
interactions is very important in many areas of
science:
such
as
surface
science1-2,
3-4
5,6
electrochemistry , and biology . In environment,
COOH of humic acid plays a crucial role in
speciation, transport and deposition of metal ions7-10.
It is one of the important groups leading to the
reactivity of humic substances11-13. Furthermore, trace
metals could interact with humic substances as a
result of electrostatic attraction and/or formation of a
chelate structure to a charged COO group12. COOH of
both formic and carboxylic acids possess potentially
two proton binding sites namely OH and C=O groups.
Proton bound clusters are known to form hydrogen
bounded networks14. Many proton bounded clusters
have been investigated experimentally15,16 as well as
througth molecular modelling17,18. The existence of
COO νas around 1535 cm-1 and νs around 1424 cm-1 is
a characteristic feature of Ca++ bounded Calmodulin
and Parvalbumin19-21. The spectra of K, Na, Mg and
Ca caroxylate were studied earlier, experimentally as
well as via molecular modelling22. Molecular
modelling was used to study COOH among different
structures. The model B3LYP/6-31G(d,P) was used to
obtain the vibrational spectra of carboxyl in case of
acetic acid, polyacrylic acid as well as benzoic acid23.
Ab initio calculations were used to study the interface
between titanium oxide and amino acid in solution24.
Both ab initio and Density Functional Theory (DFT)
were used to predict the 1:1 complexes of formic acid
with pyrrole or imazole25. Both FTIR and DFT were
used to study the spectra of monomeric glycolic
acid26. Twelve triple complexes of nine adenine
tautomers with carboxylate ion of acetic acid and
sodium ion were studied by DFT method27. Both
infrared and ab initio of the hydrogen bonding
between formic acid and water were studied. The
complex formation resulted in red shifts in the C=O
and O-H stretching vibrations and a blue shift in the
C-O stretching vibration of formic acid28. Vibrational
mode analysis on mechanism of the pyrolysis of
formic acid in the gas-phase catalyzed by water dimer
or formic acid itself was proposed29. Infrared spectra
of bicyclic and tricyclic amidine derivatives of alanine
were computed. The correlation between the
calculated and experimental vibrational frequencies
was characterized by the coefficients of 0.9997 for
DFT methods; and 0.9992 for HF (Ref.30). The
geometric
and
electronic
structure
of
1,8-bis(dimethylamino)-4-cyano-naphthalene and its
mono-protonated cation have been investigated by
DFT and time dependent density functional theory
methods31 (TD-DFT). Both IR and Raman
spectroscopic studies of salicylic and salicylate
derivatives in aqueous solution were conducted32, and
results were compared with DFT. The intramolecular
hydrogen bonding of salicylic acid was further
studied33. Both kinetic and chemical modification
analysis suggested that carboxylate and carboxyl
groups are involved directly in the enzymatic
reaction of -glucosidases34-35. Enzyme avoids
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INDIAN J PURE & APPL PHYS, VOL 43, DECEMBER 2005
unstable charged intermediates in reaction by having
groups appropriately located to donate or accept a
proton36. In almost all cases, a proton is abstracted
from a carbon adjacent to carbonyl, carboxylic acid or
carboxylate anion group by an active site residue
because the -protons are acidic by virtue of the
resonance stabilization of the enolic intermediate37.
In this work, both FTIR and DFT are utilized to
study carboxyl group in case of acetic acid, potassium
and sodium acetate, glycine, sodium salicylate,
salicylic acid and cellulose acetate. Furthermore,
carboxyl group of formic acid, carboxylic acids
R-COOH, monovalent alkali carboxylate CH3COOM, alanine, benzoic acid and naphthalene have been
investigated using DFT.
2 Experimental Details
Glycine was delivered from BDH, England. Both
sodium salicylate and salicylic acid were produced
from VEB, Germany. Acetic acid 95.0% solution and
cellulose acetate powder are the products of SigmaAldrich, Germany. Both potassium and sodium
carboxylates were obtained from the reaction of acetic
acid with their hydroxides at pH 6.0.
3 Results and Discussion
Carboxyl group was studied experimentally in case
of acetic acid, potassium and sodium acetates,
salicylic acid, sodium salicylate, glycine as well as
cellulose acetate. It is important to point out that band
assignment is achieved by comparing the eigenvectors
and intensities of the calculated bands with those
observed by FTIR. DRIFT spectroscopy was used to
study liquid phase to avoid interference due to
moisture (water molecules) over the range 1520 to
1700 cm-1. Furthermore, the KBr discs were dried
before analyses for the same reason.
Figure 1(a) presents the infrared spectra of acetic
acid in liquid phase. The assignment of acetic acid has
been discussed elsewhere23. The main spectral
characteristics of acetic acid are two sharp bands at
1276 cm–1 corresponding to C-C vibration and at 1709
cm–1 corresponding to C=O symmetric stretching. A
band at 1440 cm–1 is assigned as C-H in-plane
bending and C-H out-of-plane bending at 960 cm–1.
Figure 1(b) presents the infrared spectra of both
The IR-spectra of acetic acid, potassium, sodium
carboxylates and salicylic acid are measured with
BRUKER EQUINOX 55 Fourier Transform
Interferometer, with a direct attachment of diffuse
reflectance infrared fourier transform spectroscopy
(DRIFT), at Juelich Research Center, Germany. The
spectral range of which is 370-7500 cm-1. The
remaining spectra were recorded using KBr pellet,
with a fourier transform IR spectrometer JASCO,
FTIR- 300 E, its spectral range is 400-4000 cm-1, at
National Research Center, Egypt.
All calculations were performed with the Cache
program, at Spectroscopy Department, National
Research Center, Egypt. The geometries were
optimized using Local Spin Density treatment of
Vosko, Wilk and Nusair VWN-LDA, with DZVP
basis set. Thereafter a force constant calculation was
performed to obtain the infrared frequencies and the
corresponding infrared intensities (vibrational spectra
were performed in the harmonic approximation).
Furthermore, the assignment of the vibrational modes
was performed by visualization of the eigenvectors.
The errors within this type of calculations including a
significant part of anharmonicity corrections, can be
avoided using empirical scale factor38.
Fig. 1–FTIR spectrum of a⎯carboxylic acid liquid phase and bpotassium and sodium acetate liquid phase
IBRAHIM et al.: DFT AND FTIR SPECTROSCOPIC STUDY OF CARBOXYL GROUP
913
sodium and potassium acetates. Smith39 stated that, as
alkali metal bonded to carboxyl instead of hydrogen
bonding, the resulting arrangement is becoming
unusual producing two-bond and half-linkages which
can stretch asymmetrically and symmetrically
producing two intense bands. The asymmetric COO
stretching is obtained at 1557.2, 1559.4 cm–1 and the
symmetric COO is obtained at 1412.0, 1410.6 cm–1
for both Na and K acetates, respectively. It is worth
mentioning that the intensity of both COO bands is
due to the strong dipole moment of the carbon-oxygen
bonds.
Figure 2(a) presents the infrared spectra of salicylic
acid. From Fig.2(a) we can notice the O-H stretching
of the acid at 3300 cm–1, the aromatic C-H appears at
3064 cm–1, two C=O stretching at both 1753 cm–1 and
1668 cm–1, followed by two aromatic ring modes at
1604 cm–1 and 1575 cm–1. Then, the in-plane O-H
bending for the acid appears at 1418 cm–1, the methyl
umbrella mode at 1369 cm–1, C-O stretch at
1305 cm–1, the saturated ester C-C-O at 1188 cm–1
followed by O-C-O at 1094 cm–1 and the O-H
bending out-of-plane of the acid, at 917 cm–1, and
finally, the out-of-plane C-H bending aromatic at 755
cm–1. The infrared spectrum of sodium salicylate is
illustrated in Fig. 2(b). Special interest is directed to
the symmetric and asymmetric COO bands at 1579.4
cm–1 and 1485.9 cm–1, respectively. The shift from
1753 cm–1 (C=O) to 1579.4 cm–1 (COO) is
corresponding to changing the carboxyl group into
carboxylate with a change in its bond arrangement
into one and half linkage. The recorded shift agrees
with those shifts in case of acetic acid and both Na
and K acetate. This assignment is in a good agreement
with Brian’s39.
Glycine is the simplest amino acid and is quite
abundant in various proteins and enzymes. Glycine in
its solid form is studied in the spectral range 3000 500 cm-1. Figure 3(a) illustrates the spectrum of
glycine. A weak band corresponding to symmetric
CH stretching appears at 2898 cm−1, followed by a
combination band (697 and 1413 cm−1) at 2123 cm−1.
C=O stretching plus other vibrations are seen at 1703
cm−1. The band NH2 scissoring appeared at 1610
Fig. 2–Vibrational spectrum of a⎯ Salicylic acid and b- Sodium
salicylate
Fig. 3–.Infrared vibrational spectrum of a⎯ Glycine and b Cellulose acetate
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INDIAN J PURE & APPL PHYS, VOL 43, DECEMBER 2005
cm−1. CH2 bending beside OH bending at 1521 cm−1.
CH2 scissoring appeared at 1413 cm−1. A band
consists of both NH2 twist and CH2 twist at 1333
cm−1. A band at 1033 cm−1 can be assigned to the C-N
stretch in addition to C-C vibration. Again, a band at
892 cm−1 appears with two vibrations namely NH2
twist and CH2 twist. Finally, a band at 698 cm−1 is
assigned to NH2 bending. The band assignment of
glycine is in good agreement with Kumar et al.40
assignment.
Figure 3(b) presents the infrared spectrum of
cellulose acetate. A strong broad band at 3454.9 cm−1
is assigned to OH stretching. The band at 2959.2 cm−1
is C-H stretching of CH3 which is followed by a weak
band at 2891 cm−1 corresponding to C-H stretching of
CH2. The band can be assigned to the acetyl group on
the polymeric chain at 1757.8 cm−1 (of the C=O)
followed by the asymmetric stretching of C=O at
1632.5 cm–1. The medium intensity band at 1382 cm−1
is related to the angular distortion of the CH in the
ester methyl group41. The C-O symmetric stretching
appears at 1238.1 cm−1 and the asymmetric C-O-C
band at 1161.0 cm−1. Finally, two bands appear at
1034.6 and 901.6 cm−1 assigned to C-O and C-H,
respectively.
3.1Calculated vibrational spectra of carboxyl group
Table 1 presents the calculated infrared spectra of
carboxyl group. Carboxyl group is first optimized
then vibrational spectrum is calculated both at
VWN/DZVP level. In Table 1, there are six
vibrational modes corresponding to the carboxyl
group. The bands are obtained at the frequencies,
574.1, 660.3, 1002.9, 1232.9, 1767.9 and finally at
3398.8 cm–1. The vibrational modes are assigned to
C-OH torsion, C=O out-of-plane bending, OCO
deformation, C-O stretching, C=O stretching and OHstretching, respectively. All the vibrational modes are
corresponding to A′ symmetry, except the mode OCO
deformation which is corresponding to A″ symmetry.
The calculated infrared intensities were 32.17, 123.83,
160.63, 1.18, 310.63 and 13.46 km/mole.
The calculated infrared intensity indicates that C=O
symmetric stretching is the characteristic band of the
carboxyl group which is in good agreement with
experimental results. As a result, the spectroscopic
behaviour of the carboxyl group will be discussed in
terms of the characteristic band. Figure 4 shows the
studied structures, which contains carboxyl group. In
Table 1⎯ Infrared vibrational frequency in cm-1, infrared
intensity in km/mole and the band assignment of free carboxyl
group which weere calculated using VWN/DVZP model
Frequency, cm-1
A′
A′
A″
A′
A′
A′
574.1
660.3
1002.9
1232.9
1767.9
3398.8
Infrared intensity
Assignment
32.17
123.83
160.63
1.18
310.63
13.46
C-OH torsion
C=O op-bend
OCO deform
C-O stretch
C=O stretch
OH stretch
Fig. 4– Schematic diagram of the studied structures that contain carboxyl group namely: a⎯Formic acid, b⎯ Carboxylic acid R-COOH,
c⎯ Alkali metal acetate d⎯Benzoic acid, e⎯Glycine, f⎯Alanine, g⎯Naphthalene and h⎯Salicylic acid. Where R= CH3, CH3CH2,
CH3(CH2)2, CH3(CH2) 3, CH3(CH2) 4 and M =Li, Na, K, Rb, Cs and Fr respectively
IBRAHIM et al.: DFT AND FTIR SPECTROSCOPIC STUDY OF CARBOXYL GROUP
Table 2⎯ Calculated C=O symmetric stretching in cm-1 for
formic acid, and carboxylic acid R-COOH using VWN/DZVP
model
Structure
HCOOH
COOH
CH3COOH
CH3CH2COOH
CH3CH2CH2COOH
CH3CH2CH2CH2COOH
CH3CH2CH2CH2CH2COOH
C=O stretching, cm-1
1783.3
1767.9
1746.2
1740.1
1737.2
1735.4
1736.3
Table 3⎯ Calculated C=O symmetric stretching in cm-1 for
glycine, alanine, benzoic acid, naphthalene and salicylic acid
using VWN/DZVP model
Structure
Free carboxyl
Alanine
Benzoic acid
Naphthalene
Salicylic acid
Glycine
C=O stretching, cm-1
1767.9
1738.3
1711.8
1706.2
1748.4 and 1658.4
1614.3
the case of free carboxyl, each structure is optimized
and the vibrational frequencies are calculated using
VWN/DZVP model.
Carboxyl group is optimized in case of formic acid,
as well as carboxylic acids R-COOH, where R varies
from CH3 to CH3(CH2)4, respectively. Generally, the
optimized carboxylic acids structures are Cs symmetry.
The characteristic band C=O is compared with that of
free carboxyl. As in Table 2, C=O of carboxyl group is
at 1767.9 cm–1, the band is shifted up to 1783.3 cm–1 in
case of formic acid. C=O showed a shift from 1746.2
cm–1 to 1736.3 cm–1 ongoing from CH3COOH to
CH3(CH2)4COOH, which means that only 9.9 cm–1 shift
is regarded as a result of hydrocarbon chain effect on
carboxyl group of R-COOH, while the shift is 31.6 cm–1
as compared with C=O of free carboxyl.
Table 3 shows C=O of carboxyl in case of another
five structures namely: Glycine, alanine, benzoic acid,
naphthalene and salicylic acid. A noticeable change in
the C=O is recorded in case of alanine, which is
shifted to 29.6 cm–1. Another shift of 56.1 cm–1
corresponds to benzoic acid. While the characteristic
band in case of naphthalene is calculated at 1706.2
cm–1 with a shift of about 61.7 cm–1. Finally, salicylic
acid has two bands at 1748.4 and 1658.4 cm–1. Then
C=O of glycine is 1614.6 cm–1 with a shift of 153.6
cm–1. It is clear that C=O of the studied structure is
shifted to lower frequencies as compared with free
carboxyl. It is worth to mention that, at VWN/DZVP
level of theory negative frequencies were obtained for
915
Table 4⎯ Effect of alkalies on the characteristic band of
carboxyl group
Structure
CH3COO-Li
CH3COO-Na
CH3COO-K
CH3COO-Rb
CH3COO-Fr
CH3COO-Cs
C6H4(OH)-COO-Na
C6H5COO-Na
HCOO-Na
CH3CH(NH2)-COO-Na
CH3CH2COO-Na
CH3CH2CH2COO-Na
Asymmetric
COO stretching
Symmetric
COO stretching
1505.2
1520.8
1531.6
1533.2
1529.9
1547.1
1575.6
1566.4
1535.2
1520.4
1516.2
1513.6
1352.2
1361.2
1348.0
1345.1
1303.0
1352.2
1325.2
1349.8
1301.4
1373.0
1362.4
1356.1
Table 5⎯ Effect of hydrocarbon chain and aromatic cycle on
the characteristic band of carboxyl ions
Structure
C6H4(OH)-COO
CH3CH(NH2)-COO
CH3COO
C10H8-COO
C6H5COO
C=O stretching, cm-1
1745 and 1652.0
1629.8
1615.2
1612.4
1499.3
cellulose acetate. The negative sign indicates that the
vibrational spectrum is calculated for the transition
state not for the optimum structure. Accordingly, the
vibrational spectra of cellulose acetate is not
considered at this level of theory.
The effect of six monovalent alkalis on COOH
vibrations was studied. The results of COO of the
studied alkali carboxylate are given in Table 4. The
frequency of asymmetric COO is increasing slightly
from Li up to Cs. COO symmetry shows the same
behaviour with an exception that Na and Cs show higher
values. Another effect on COOH is tested as sodium is
coordinated instead of hydrogen to formic acid, alanine,
benzoic acid, salicylic acid and two R-COOH structures.
The calculated data are compared with COO of sodium
carboxylate which are 1520.8 cm–1 and 1361.2 cm–1,
respectively. Results in Table 4 indicate a shift of 19.0
cm–1 in symmetric COO while going from HCOO-Na to
CH3CH2-Na, followed by a shift in case of CH3(CH2)2Na at about 2.6 cm-1. COO asymmetric stretching of
alanine is 1520.4 cm-1 which is similar to that of sodium
carboxylate, while COO symmetric is lower than that of
sodium carboxylate by 11.8 cm-1. Regarding both
salicylic and benzoic acids, COO asymmetric stretching
shows a respective shift of 54.8 and 45.6 cm-1 towards
high frequency. The COO symmetric stretchings are in
contrast to those showing a respective shift towards
lower frequency.
INDIAN J PURE & APPL PHYS, VOL 43, DECEMBER 2005
916
Table 6⎯ Comparison between experimental spectra in
cm-1of glycine with their VWN/DZVP calculated values
Experimental IR
Calculated IR
Assignment
2898
2123
1703
1610
1521
1413
1333
1033
2919.2
1614.3
1610.0
1509.9
1377.0
1325.0
1094.5
892
692
899.0
683.0
CH symmetric stretching
Combined band
C=O stretching
NH2 scissoring
CH2 bend + OH bend
CH2 scissoring
NH2 twist + CH2 twist
C-N stretching + C-C
vibrations
NH2 twist + CH2 twist
NH2 bend
Table 5 presents the results of carboxylate ion in
case of acetic acid, alanine naphthalene and salicylic
acid. Negative frequencies were obtained in case of
glycine, this indicates that the glycine structure is a
transition state hence the optimum structure was not
found at this level of theory. Generally, the results
show that, C=O values of the carboxylate ion are
lower as compared to carboxyl group of the same
structures. Furthermore, carboxylate ion frequencies
can be arranged according to the following decreasing
order:
Salicylic acid > alanine>
Naphthalene>benzoic acid.
acetic
acid
>
3.2Comparison between experimental and calculated spectra
Table 6 presents both calculated and experimental
vibrational modes of glycine. The optimized glycine
molecule has Cs symmetry. Comparison of the results
reveals that calculated vibrational modes are in good
agreement with the FTIR results. Furthermore,
modelling with DFT is considered to be a good tool
for the bands assignment of molecules containing
carboxyl group.
4 Conclusion
Carboxyl group was subjected to both experimental
as well as modelling study. Hydrocarbon chain like RCOOH has a shift in their characteristic band of
carboxyl group slightly towards lower frequency. As
compared with acetic acid (with the exception of both
formic acid and free carboxyl group), all structures
show a shift in their characteristic bands towards
lower frequencies. This shift is slightly noticeable for
R-COOH, alanine, benzoic acid and for naphthalene,
while decrease is more in case of salicylic acid and
glycine, and becomes significant in case of
carboxylate ion. Alkali acetate shows a shift of about
200 cm-1 towards the lower frequency as a carboxyl
ion is transformed into carboxylate. The calculated
frequencies for some bands may be considered as of
slightly overestimated values and the difference may
be related to the anharmonic effect, which is avoided
by scaling the calculated frequencies with empirical
scale factor. In spite of this, calculation based on the
DFT method shows good agreement with
experimental results. Hence, it could be concluded
that, COOH in both aliphatic and/or aromatic
structures acts as a model system to verifying the
usefulness of DFT method of calculation.
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