Page 1
Density functional Computations, FT-IR, FT-Raman, NMR and UV analysis of
3-Formyl-2-thienylboronic acid
Parveen begaum. K, Prabhu. T* , Jayasheela. K, Periandy. S, Roopakala. K, Sowbakkiyavathi. E. S
1,2 Department of physics, A.V.C. College (autonomous), Mayladuthurai, Tamilnadu, India.
3,4,5,6 Department of physics, Kanchi mamunivar center for post graduate studies (autonomous), Puducherry, India.
*Corresponding Author E-mail: [email protected]
Abstract
3-Formyl-2-thienylboronic acid was investigated by spectral and quantum
chemical computational methods. The solid phase FT-IR and FT-Raman spectra were
recorded in the region 4000-400 cm-1
and 3500-50 cm-1
respectively. The conformation,
molecular geometry and vibrational frequencies of title molecule have been calculated
by using the density functional method B3LYP with 6-311++G (d,p) basis set. The13
C
NMR and 1H NMR were calculated by using the gauge independent atomic orbital
(GIAO) method in combination with B3LYP functional and the 6-311++G (d,p) basis
set and the results were analysed in comparison with recorded experimental spectra. A
study on the electronic and optical properties; UV absorption wavelengths, excitation
energy, dipole moment, polarizability and hyper polarizability were also made using
NBO and HOMO-LUMO methods. The possible electronic transitions, donor and
acceptor orbitals were predicted by NBO method. The thermo dynamical parameters
and molecular electrostatic potential mapping were predicted theoretically and
discussed.
Key words: FT-IR, FT-Raman, NMR, UV analysis, B3LYP, molecular docking
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/199
Page 2
Introduction
The molecule 3-Formyl-2-thienylboromic acid comes under Boronic acid group whose
distinctive electronic and chemical properties made this class of compounds pertinent for
application in a variety of biomedical field. As they possess a vacant p-orbital they behave as
organic Lewis acids. Under physiological conditions boronic acids effortlessly adapt to anionic
tetrahedral structure (sp3 boron) from neutral and trigonal planar structure (sp2 boron). Broad
reactivity profile, stability and lack of apparent toxicity makes boronic acids a predominantly
fascinating class of synthetic intermediates. Low toxicity and eventual degradation into the
environment friendly boric acid, boronic acids can be viewed as ‘‘green’’ compounds [1]. A wide
variety of boronic acid derivatives of divergent biologically important compounds have been
synthesized as anti-metabolites for a possible two-pronged attack on cancer [2]. In addition to
inhibition of tumor growth, the use of boron for neutron capture therapy would be possible owing
to the preferential localization of boron compounds in tumor tissues. Boronic acid analogs have
been synthesized as transition state analogs for acyl transfer reactions [3]. Boronic acid and its
derivatives have been investigated by several authors [ 1- 4]. Molecular structure of phenyl
boronic acid has been investigated by Rettig and Trotte [4]. However, the molecule 3-Formyl-2-
thienyl boronic acid has not been subjected to the complete quantum computation analysis
supported by experimental spectral data, hence the present study has been undertaken to do the
complete vibrational, structural, NMR and UV analysis of the title molecule.
Experimental studies
The titled compound is purchased from Sigma–Aldrich Chemicals which is of
spectroscopic grade and hence used for recording the spectra as such. The FT-IR spectrum of
the above compound is recorded in Bruker IFS 66V spectrometer in the range of 4000–400
cm−1
. The spectral resolution is ±2 cm−1
. The FT-Raman spectrum of the above compound is
also recorded in the same instrument with FRA 106 Raman module equipped with Nd:YAG
laser source operating at 1.064 μm line widths with 200 mW power. The spectra are recorded
in the range of 3500-50 cm-1
with scanning speed of 30 cm−1
min−1
and spectral width 2 cm−1
.
The frequencies of all sharp bands are accurate to ±1 cm−1
.
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/200
Page 3
Theoretical studies
All quantum calculations of 3-Formyl-2-thienyl boronic acid were performed with
Gaussian – 09W program package [5] on Pentium IV processor personal. The optimized
geometrical parameters of the title molecule were determined using density functional theory
(DFT) by B3LYP methods and 6-311++G(d,p) basis sets. The vibrational frequencies of
Formyl-2-thienylboromic acid were calculated with the same functional and two basis sets 6-
31++G(d,p) and 6-311++G(d,p) . In order to improve the agreement between the calculated
frequencies and the experimental frequencies, the calculated frequencies were scaled down as
suggested in literatures and the scaling factors were reported. The charge distribution of the
molecule were computed with 6-311++G(d,p) basis set. The electronic absorption spectra of
the compound was simulated with B3LYP/ 6-311++G(d,p) level in gas phase and solvent
(DMSO and ethanol) phases. Natural Bond Orbital (NBO) analysis was carried out using
NBO version 3.1. The NMR chemical shifts of the compound were also calculated using the
Gauge Independent Atomic Orbital's (GIAO) method along with B3LYP/6-311++G (d, p)
combination. The energy distribution from HOMO to LUMO, Mullikan charges and dipole
moment of the title molecule are also computed using B3LYP method with same basis set.
Result and discussion
Geometrical Analysis
The geometrical structure of the molecule along with the numbering of atoms of title
molecule is shown in Fig. 1. The global minimum energy obtained by DFT method with
functional B3LYP and basis set 6-311++G(d,p) is -841.2 Hartree. The optimized geometrical
parameters are presented in Table 1.
Fig. 1 Molecular geometry of 3-Formyl-2-thienyl boronic acid
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/201
Page 4
As shown in the table, the CC bond lengths in the five membered thiophene ring
vary from 1.37 – 1.42 Å; C1-C2 (1.39 Å) , C2-C3 (1.42 Å), C3-C4 (1.36 Å) , in which 1.39 Å
and 1.36 Å are closer to benzene CC value 1.38 Å, that shows there is a kind of conjugation
even within thiophene ring but differs slightly from that of benzene. C2-C3 (1.42 Å) value is
close to pure single bonded CC value which shows the conjugation at this point is disturbed
by CO group. The bond length C2-C14 is 1,33Å which is purely a double bonded CC value
which implies whose electronic charge density is altered by the CO group. The literature
value for C-S bond length is 1.70 Å [7-8], in this molecule there are two CS bonds, both are
1.72 Å that shows there is slight rearrangement of electronic charge distribution due to the
presence of them within the ring.
The expected C-Br bond length value is1.6 Å, in present compound C1-B8 is found to
be 1.573 Å, this is slightly less than the expected value which may be due to the withdrawal
of charges from this bond to adjacent B-O bonds. The bond length of two B-O bonds in this
molecule are 1.36 Å and 1.355 Å, which shows there is asymmetrical charge distribution
among these bonds which may be due to the uneven influence of S atom structurally. This is
also reflected in the two OH length values; the values of O9-H11 and O10-H12 are found to
be 0.96 and 0.97 Å respectively. All the CH in the ring structure is expected to be of the
length 1.08 Å [8]. In the present compound, CH bonds are having the bond length values
between 1.087-1.09 Å which shows the variation in the conjugation in thiophene ring.
The bond angle around each carbon atom is expected to be 120o
[10] due to SP2
hybridisation. But, in this molecule, only the bond angles C3-C2-C14 and S5-C4-H7 are
found to be 120o
as expected, but the other bond angles are varying between 93 o
-132 o
,
which means the bond angle are largely varied or hybridisations are drastically changed due
to the influence of both S and Br atoms.
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/202
Page 5
Table 1.
Optimized Geometrical parameter for 3-Formyl-2-thienylboromic acid Computed at B3LYP/6-
311++G(d,p).
Mulliken & Natural Charge analysis
The atomic charge analysis plays a substantial role in the quantum chemical
understanding of molecules because the atomic charges influence the properties of the
molecular systems, such as its dipole moment, bond strength, vibrational frequencies,
electronic transitions, chemical shifts and molecular polarizability etc. The entire compound
Bond
Length
(Å)
B3LYP/
6-311++G
(d,p)
Bond
Angle
( )
B3LYP/
6-311++G
(d,p)
C1-C2 1.3988 C2-C1-S5 109.0133
C1-S5 1.7295 C2-C1-B8 132.6805
C1-B8 1.5733 S5-C1-B8 118.3062
C2-C3 1.4285 C1-C2-C3 113.9138
C2-C14 1.3366 C1-C2-C14 125.6234
C3-C4 1.363 C3-C2-C14 120.4628
C3-H6 1.0814 C2-C3-C4 112.3568
C4-S5 1.7283 C2-C3-H6 123.0724
C4-H7 1.0795 C4-C3-H6 124.5708
B8-O9 1.3683 C3-C4-S5 111.4347
B8-O10 1.3552 C3-C4-H7 128.3184
O9-H11 0.9634 S5-C4-H7 120.247
O10-H12 0.9711 C1-S5-C4 93.2813
H12-O13 1.852 C1-B8-O9 115.6472
O13-C14 1.1938 C1-B8-O10 125.0784
O9-B8-O10 119.2744
B8-O9-H11 112.3468
B8-O10-H12 115.1534
C2-C14-O13 131.6987
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/203
Page 6
is stabilized by electrostatic forces due to the distribution of the charges on these atoms, thus
any change in electro negativity of an atom can cause wide change in the overall distribution
of charges in each atom and thus the properties of the entire molecular system. The atomic
charges were calculated by two methods for comparison purpose; Mulliken Population
analysis (MPA) and Natural atomic charges (NAC) methods. Both Mulliken and Natural
atomic charges of the titled compound were computed by B3LYP/6-311++G(d,p) method
and the values are presented in the Table 2, the same is also shown graphically in Fig 2 for
comparison.
Carbon atoms in the thiophene rings are expected to be equally negative. In present
study, NAC shows all C atoms with negative charge, but only C1 and C4 are in the range of
benzene carbon. C2 and C3 values are very less, this may be due to the influence of CO
attached with C2. But in MPA, only C1 (-0.006) is slightly negative and all other Carbon C2
(0.067), C3 (0.04) and C4 (0.017) atoms are positive, in which the withdrawal of charges are
expected from C to S atom and CO groups. But charges were found to be withdrawn from S
and B atoms in both the methods, hence C atoms which are attached these atoms B and S can
only be negative, as predicted by NAC.
Other hand C14 (0.599) is having highly positive in MPA and slightly negative in
NAC, this is the C atom which is directly bonded to O atom; hence it should be positive as
predicted by MPA rather than by NAC. All hydrogen atoms are either slightly negative or
positive in MPA, but highly positive in NAC. The NAC prediction in this case is reasonable
as the H atoms can only lose electrons to the C atoms to which they are attached.
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/204
Page 7
Table 2:
Mulliken Population & Natural atomic Charge for 3-Formyl-2-thienylboronic acid
Computed at B3LYP/6-311++G(d,p).
ATOM
MULLIKEN
POPULATION CHARGE
B3LYP/6-311++G(d,p)
NATURAL ATOMIC
CHARGE
B3LYP/6-311++G(d,p)
1 C -0.00672 -0.243
2 C 0.06760 -0.1548
3 C 0.04651 -0.1027
4 C 0.01765 -0.1924
5 S 0.00514 0.2638
6 H -0.00028 0.1149
7 H 0.00083 0.1159
8 B 0.00039 0.5336
9 O -0.0002 -0.4333
10 O 0.0060 -0.4398
11 H -0.0006 0.2438
12 H 0.0167 0.2506
13 O 0.2478 -0.3818
14 C 0.5991 -0.0750
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
1 C 2 C 3 C 4 C 5 S 6 H 7 H 8 B 9 O 10O
11H
12H
13O
14C
Mulliken charge
Natural charge
Fig.2. Mulliken and Natural Charge for 3-Formyl-2-thienylboronic acid
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/205
Page 8
NMR ANALYSIS:
Chemical shift calculations are fast, accurate and applicable for complex systems. The
chemical shifts for 1H and
13C atoms of the titled compound were computed for optimized
structure, supported by GIAO method. The computed chemical shift values in gas and solvent
phases are presented in Table 3 and graphical representations of the values are shown in
Figure 3 and 4.
The titled compound showed the chemical shifts of carbon atoms in thiophene rings
lies in the range 136 to 153 ppm. The same chemical shift values for aromatic ring carbon
atoms are expected between 120 - 130 ppm [8]. This shows that the conjugation is
appreciably altered by the presence of S atom in the ring. C1 and C4 which are attached
directly to S have the maximum shift in the ring 141 and 153 respectively. This shows that
these two carbon atoms draw electronic charges from S and thus their nuclear shielding have
been increased considerably. C2 has the least shift in the ring 132 ppm, this confirms a fact
that CO has captured some of the electronic charges from C2 due to the high electro
negativity of the O atom. These entire four carbon shift within the ring agrees well with the
charge prediction by NAC method rather than the MPA method. The C14 atom which is
directly attached with O atom in the CO group has shown the maximum shift 284 ppm. This
can be only due to the over deshielding i.e. over withdrawal of the electrons from this carbon
atom C14 by the attached O atom. This is completely in agreement with high positive charge
of MPA method, the prediction of slightly negative charge by NCA method is not found
suitable here.
The 1H NMR spectra interpretation is very significant when attempt is made to
measure the possible effects of highly electro negative atoms on protons [10]. The usual
scale, for PMR (Proton Nuclear Magnetic resonance) studies is about 7 to 8 ppm in aromatic
ring, between 2 to 3 for aliphatic chain. In the present study, all the H NMR chemical shift
values are in good agreement with expected range 7 to 8 ppm for aromatic ring. Thus, it is
clear the conjugation in thiophene ring is also very close to benzene ring as structural and
atomic charge analysis. But 11H and 12H which are attached to O atoms directly in boronic
acid group shows chemical shift 3.9 and 3.6 ppm respectively. Actually these hydrogen atoms
are in the aliphatic chain, hence they are expected in the range 1to 2 ppm, since they are
attached with O, their values have been enhanced due to de shielding.
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/206
Page 9
Table. 3.
Calculated 13
C NMR &1H Chemical Shifts (ppm) for 3-Formyl-2-thienylboronic acid
Computed at B3LYP/6-311++G(2d,p) GIAO.
Atom
Gas
CDCl3 Atom
Gas
CDCl3
13
Carbon 1Hydrogen
1C 152.86 153.216 6H 7.812 7.9501
2C 136.09 136.027 7H 7.563 7.7946
3C 141.068 141.436 11H 3.642 3.9664
4C 141.527 143.146 12H 3.421 3.625
14C 285.284 284.575
Fig.4. Theoretical H NMR spectra for 3-Formyl-2-thienylboronic acid
Fig.3.Theoretical C NMR spectra for 3-Formyl-2-thienylboronic acid
4 5 6 7 8
0.0
0.5
1.0
de
ge
na
racy
chemical shift
120 140 160 180 200 220 240 260 280 300
0.0
0.5
1.0
de
ge
na
rary
chemical shift
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/207
Page 10
VIBRATIONAL ANALYSIS:
The titled molecule under investigation has 14 number of atoms and thus 36 normal
modes of fundamental vibrations. Vibrational wave numbers for all the fundamental modes
of the titled compound are computed using B3LYP functional and 6-311++G (d,p)basis set
and the values along with the experimental data are presented in Table 4. The FT-IR spectra
& FT Raman of the titled compound are shown in Figure 5.
OH Vibrations
There is double OH in the boronic acid group, the stretching vibration due to these
bands is expected in the range 3700 – 3300 cm-1
[11]. The OH group vibration are likely to be
the most sensitive to the environment, so they show pronounced shifts in the spectra of the
hydrogen bonded species. The bands corresponding to OH stretching in this molecule is
observed at 3330 and in FT IR and 3300 in FT Raman respectively, theoretically these values
are obtained at much higher values. The presence of the peak at the higher end implies there
will be intermolecular Hydrogen bonding due to these OH group, however in this molecule in
the experimental spectra the peaks are only around 3300 cm-1
which means there won’t be
hydrogen bonding with this molecule due to this OH group.
OH in-plane bending band is expected at 1451cm-1
[12], this is observed at 1450 cm-1
in FT-Raman spectra and at 1349 cm-1
in FT-IR spectra. Similarly, the out of plane bending
modes are expected between 710 – 517 cm-1
, this is observed at 640 and 610 cm-1
in FT-IR
and FT-Raman in the present case. This deviation is generally expected at the out of plane
bending modes, as the interaction between various modes at this lower range is very stronger,
the bands are very close to each other at these ranges.
CH Vibrations
The titled molecule has two CH stretching vibrations. These aromatic CH stretching
usually show peaks in the characteristic region 3100 –3000cm−1
[13,14]. Aliphatic C-H
stretching vibrations lie between 3000- 2900cm-1
. In this molecule, there are only two
aromatic CH bonds, whose bands are observed at 3103, 2979 in FT-IR. These vibrations
indicate they are closer to aromatic CH values, which confirms the predictions in the previous
sections; structural and chemical shift analyses.
The C-H in-plane bending mode usually occurs as strong to weak bands in the region
of 1300 to 1200 cm-1
[14]. Experimental study of the title compound show that the C-H in-
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/208
Page 11
plane bending vibrations lie at 1384 to 1208 cm-1
in FT-Raman and FT-IR spectrum
respectively. The C-H out of plane bending vibrations are expected to occur as strong to weak
intensity bands in the region of 800-600 cm-1
[15]. The recorded FT-IR spectrum of the titled
molecule showed bands at 605 and 580 cm-1
. All these bending modes are in the expected
region, though the out of plan bending modes lie at the bottom end of the expected region
which is due to the overlapping of the CO bending modes.
THIOPHENE RING VIBRATIONS
The aromatic ring CC stretching vibrations occur generally in the region 1600-1350
cm-1
. The position and the intensity of the ring stretching bands of five member rings of
hetero atoms are more sensitive than the corresponding bands of benzene [16]. In the present
study, there is one double bond CC and three single bond CC stretching modes and they are
observed at 1506 , 1399, 1374 and 1245 cm
-1 respectively. The CC double bond lies outside
ring, hence its values are found less than its expected value 1600 cm-1
. The three CC values
within the ring is also less when compared to benzene ring values, greater than 1400 cm-1
,
this is due to the weakening of the bond due to the presence of S in the ring. All these values
are in good agreement with the theoretical wave numbers. Both the bending modes are
slightly deviated from the expected range, which indicates that they are not pure like
stretching which means lot of influence of other modes (CC & CO) occurs in this region.
The C-S stretching vibration is difficult to identify as it usually appear weak in FT-IR
spectrum. The absorption of C-S bond is found in the range 1000 to 800 cm
-1 for both
aliphatic and aromatic sulfides. These CS bands are observed in the present molecule at
wave numbers 910 and 853 cm-1
, any deviation in the wave number must be due to the five
member thiophene ring structure only.
C=O VIBRATIONS
The stretching mode of C=O group is expected in the range of 1750 to 1730 cm-1
.In
the present study, the C=O stretching band is observed at 1750 cm-1
both in the FT-IR and
FT-Raman spectra as a very strong band. This value is exactly the expected value which
shows this band remain undisturbed by any influence in this molecule. The C=O in-plane
and out-of-plane bending modes are expected in the region 625 ± 70 and 540 ± 80 cm-1
respectively [17-18].The calculated wave number for the C=O in-plane bending mode of the
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/209
Page 12
title compound appeared at 670 cm-1
and C=O out-plane bending mode is at 543 cm-1
.These
observed deviation from the expected value explains the presence of high positive and
negative potential, where the C=O group is present, causing the enhanced biological activity
of the molecule.
AVC-A2-
Name Description
4000 4003500 3000 2500 2000 1500 1000 500
100
0
10
20
30
40
50
60
70
80
90
cm-1
%T
1652.19cm-1
1349.28cm-1
753.24cm-1
1437.61cm-1
1399.51cm-1
1374.37cm-1
1208.10cm-1
1506.96cm-1
721.56cm-11070.24cm-1
853.66cm-1
3332.90cm-1 1110.20cm-1
589.75cm-1
670.78cm-12979.35cm-1
3103.26cm-1
640.97cm-11015.00cm-12892.77cm-1
991.17cm-1
910.56cm-1
2519.82cm-12425.19cm-1
2362.97cm-1
2337.20cm-1
484.66cm-12186.29cm-1
1810.79cm-1
3953.58cm-1
3925.57cm-1
3799.46cm-1
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/210
Page 13
Table.4.
Experimental FT-IR, FT-Raman and Calculated DFT B3LYP/6-311++G(d,p)
levels of vibrational frequencies (cm1
) of 3-Formyl-2-thienylboronic acid
No
frequencies (cm-1
)
VEDA Observed Calculated Assignment
IR Raman Un
scaled Scaled
1 3330 3847 3712 ν OH ν OH 100
2 3300 3664 3521 ν OH ν OH 100
3 3103 3245 3118 ν CH ν CH 91
4 2979 2976 3214 3088 ν CH ν CH 91
5 1750 1750 1851 1778 ν O=C ν OC 94
6 1506 1519 1459 ν C=C + β CH ν CC 13+ β CH 44
7 1399 1449 1392 ν CC ν CC 18
8 1374 1372 1422 1366 ν OB ν OB 42
9 1349 1384 1330 ν CC+ β CH ν CC 13+ β CH 26
10 1245 1322 1270 ν CC+ ν OB ν CC 17+ ν OB 17+OH 17
11 1208 1209 1161 β OH ν CC 22+ β OH 27
12 1110 1134 1089 β CC β OH 14+ β CC 16
13 1070 1102 1059 β CC β OB 27+ β CC 23
14 1040 1039 998 β OB β OB 47
15 1015 1007 967 β OB β OB 23
16 991 964 926 ν CS ν CS 15
17 910 913 877 ν CS ν CS 45
18 853 850 840 807 β CS β CS 85
19 753 750 753 723 β CS β CS 13
20 721 714 686 β CB β CB 45
21 670 706 678 β CO β CO 56
22 640 685 658 γ OH γ OH 53
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/211
Page 14
23 610 617 592 γ OH γ OH 25
24 605 606 582 γ CH γ CH 68
25 589 580 582 559 γ CH η CCCC 15
26 543 546 524 γ CO β CCO 34
27 484 474 455 γ CC η CCCC 64
28 450 460 442 γ CB ν CB 16
29 390 374 γ CS η CSCC 20
30 326 313 γ CS β OBO 26
31 259 248 γ OB η HOBC 17
32 232 222 Β OCB β CBO 53
33 184 176 β OBO β OBO 31
34 177 170 β CCC η CCCO 25
35 109 104 β CCC β CCC 64
36 70 67 β CSB β BCS 64
-stretching, δ -in-plane bending, γ-out-of-plane bending, -scissoring, -rocking, -twisting, δring-
in-plane bending ring, γring-out-of -plane bending ring.
NBO ANALYSIS:
Natural bonding analysis (NBO) is an effective tool for determining the chemical
interactions, charge distribution and electron transfer from filled donor or bonding orbitals or
lone pair orbital to vacant acceptor or anti bonding orbitals. The density functional theory is
used to analysis these bonding and anti-bonding interactions, by means of the second-order
perturbation theory, interms of stabilization energy (E(2)
) [19]. This energy represents the
estimation of the off-diagonal NBO Fock matrix elements, which can be determined from the
following relation [20];
2(2) ( , )
ij i
j i
F i jE E q
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/212
Page 15
where qi is the donor orbital occupancy, εi and εj are the energy in the donor and acceptor
levels and F(i,j) is the off diagonal Fock matrix elements.
In this study, the charges transferring from bonding to anti-bonding levels were
analyzed. The intermolecular hyper conjugative interactions are caused by the orbital
overlapping between n and *&* orbitals. The E(2)
values indirectly indicate the probability
of transitions, accordingly for this molecule there are seven highest possible transitions,
which are listed below in the descending order for comparison. The other important
transitions in this molecule are listed in Table 5.
From this study, the top ten probable transitions in this molecule are S5→C1-C2
(12.73 KJ/Mol , n to π*), S5→C3-C4(10.35 KJ/Mol , n to π*), C1-C2 →O13-C14 (9.54
KJ/Mol , π to π*), C1-C2→ C3-C4 (8.49 KJ/Mol , π to π*), C3-C4 →C1-C2 (7.8KJ/Mol , π
to π*), C1-S5→C2-C14 (3.42 KJ/Mol , π to ζ*), O10→C1-B8 (3.02 KJ/Mol , n to π*),
O9→B8-O10 (2.79 KJ/Mol , n to ζ*), C 1 - C 2 →O 13 - C 14 (2.66 KJ /MOL ζ to π*) ,
C 4 – S5 → C3 – H 6 (2.34 KJ /MOL ζ to ζ*)
The maximum E2 value here is 12 KJ/MOL, only the n to π* transitions have values
greater than 10 KJ/MOL, and all π to π* transitions have values in the range 10 to 7
LJ/MOL. These value of E2 are very less when compared to benzene derivatives. Thus, the
maximum probable transitions in this compound take place between sulphur atom(S) to the
antibonding acceptors π* in the ring. This measures the π delocalization within the thiophene
ring. Thus, the NBO analysis also confirms the fact that the biological activity of the
molecule is primarily due to the sulphur atoms in the thiophene rings. The electronic
transitions however can also occur entirely at unexpected region which can also be verified
theoretically and experimentally through UV-visible spectroscopy, whose principle and
discussion is presented below.
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/213
Page 16
Table. 5.
Second order perturbation theory of Fock matrix in NBO basis of 3-Formyl-2-
thienylboronic acid
Donor
Typ
e of
bon
d
Occ
up
an
cy
Acceptor
Typ
e of
bon
d
Occ
up
an
cy
En
ergy E
(2)
kca
l/m
ol
En
ergy
dif
fere
nce
E(j
)-E
(i)
a.u
. P
ola
rize
d
ener
gy F
(i,j
)
a.u
.
S 5 n 0.76942 C 1 - C 2 π* 0.20031 12.73 0.26 0.073
S 5 n 0.76942 C 3 - C 4 π* 0.1355 10.35 0.26 0.069
C 1 - C 2 π 0.88554 O 13 - C 14 π* 0.0623 9.54 0.31 0.071
C 1 - C 2 π 0.88554 C 3 - C 4 π* 0.1355 8.49 0.29 0.063
C 3 - C 4 π 0.9224 C 1 - C 2 π* 0.20031 7.82 0.29 0.064
C 1 - S 5 σ 0.98487 C 2 - C 14 σ* 0.01347 3.42 1.13 0.078
O 10 n 0.98024 C 1 - B 8 σ* 0.01614 3.02 0.98 0.069
O 9 n 0.98447 B 8 - O 10 σ* 0.01017 2.79 1.04 0.068
C 1 - C 2 σ 0.98508 O 13 - C 14 π* 0.01291 2.66 0.76 0.057
C 4 - S 5 σ 0.99039 C 3 - H 6 σ* 0.00771 2.34 1.11 0.064
O 13 - C 14 π 0.99004 O 10 - H 12 σ* 0.01029 2.24 0.85 0.055
C 3 - H 6 σ 0.98762 C 4 - S 5 σ* 0.01053 2.05 0.76 0.05
O 13 - C 14 π 0.9924 C 1 - C 2 π* 0.20031 2.03 0.41 0.041
UV-Visible spectral analysis
Theoretical UV calculations were carried out in gas phase by TD-DFT method using
B3LYP/6-311++ G(d, p) functional and basis sets in order to get a deeper perception into the
likely electronic excitations, wavelengths, oscillator strengths and major H-L contributions
of various excitations of the of the titled compound and presented in Table 6. The
experimental UV-Visible spectrum is shown in Figure 5.
In case of solvent phase, the energy gap of the cited ten top transitions are 1.73, 2.89,
3.57, 3.87, 4.09, 4.20, 4.26, 4.53, 4.75 and 5.04 eV respectively and their estimated
absorption wavelengths are 716, 428, 347, 319, 302, 294, 291, 273, 260 and 245 nm
respectively. In gas phase, the same energy gaps are 1.668, 2.946, 3.625, 3.927, 4.039, 4.325,
4.402, 4.565, 4.844, 4.97 ev and the wavelength are 742, 420, 315, 306, 286, 281, 271, 255,
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/214
Page 17
249 nm respectively. The wavelength in both phases implies that the top two transitions
(742, 420) lie only in the visible region. i.e the two n to π* transitions from S atom in the ring
are purely in the visible region. The next three π to π* (347, 319, 302) takes place at
wavelength above 300 nm. The density of states (DOS) analysis shown in Fig.5 shows that
density of states are very high only in the region 200 - 300 nm. Hence, the ζ to π* transitions
which are listed in the bottom of the top ten list are going to be very prominent in this
molecule. The oscillator strength which is the measure of the intensity of the bands also
confirms this trend, they show insignificant values for all the top five transitions in the list,
only the sixth (290 nm) and ninth (260 nm) transitions in list has considerable oscillator
strength, theoretically only these transitions can appear in the spectrum. This is also proven in
the experimental Uv-Vis spectrum where prominent peaks have appeared against the
theoretically predicted values.
Fig.5. Experimental & theoretical UV-Visible spectra & DOS spectra for 3-Formyl-
2-thienylboronic acid
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/215
Page 18
Table. 6.
Calculated and theoretical UV-Visible value of the 3-Formyl-2-thienylboronic acid
by B3LYP/6-311++G(d,p) method.
Gas phase Solvent phase (Ethanol)
λ
(nm)
E
(eV)
(f) Major Contribution
Theo. Exp.
E (eV) (f) Major Contribution λ(nm)
742 1.668 0.0008 HOMO→LUMO (95%) 716 1.730 0.0010 HOMO→LUMO (95%)
420 2.946 0.0001 H-1→LUMO (47%) 428 2.891 0.0001 H-1→LUMO (48%)
341 3.625 0.0006 H-2→LUMO (50%) 347 3.572 0.0009 H-2→LUMO (51%)
315 3.927 0.0004 HOMO→L+1 (84%) 319 3.877 0.0000 H-1→L+1 (13%)
306 4.039 0.0001 H-1→L+1 (13%) 302 4.093 0.0005 H→L+1 (88%)
286 4.325 0.0618 H-1→LUMO (44%) 294 290 4.207 0.0823 H-1→LUMO (45%)
281 4.402 0.0000 H-1→L+1 (83%) 291 4.260 0.0001 H-1→L+1 (84%)
271 4.565 0.0102 H-1→L+1 (37%) 273 4.538 0.0076 H-1→L+1 (41%)
255 4.844 0.1367 H-2→LUMO (38%) 260 260 4.759 0.2142 H-2→LUMO (41%)
249 4.978 0.0016 HOMO→L+2 (74%) 245 240 5.046 0.0022 HOMO→L+2 (87%)
HOMO-LUMO Charge transfer
The highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular
orbitals (LUMO) are the important constituent of Frontier molecular orbitals (FMO). The
HOMO energy represents the ability of electron giving; LUMO represents the ability of
electron accepting [21]; and the energy gap between HOMO and LUMO determines
molecular transport properties, chemical reactivity, electrophilic index, hardness and softness
of the molecule. The HOMO and LUMO of the molecule are computed with B3LYP function
with 6-311++ G (d, p) basis set and the pictorial diagram of the same is shown in Fig.8.
The HOMO-LUMO energy gap and different reactivity descriptors of molecule in
both levels are presented in Table 8. The calculated energy of the HOMO is -0.219 eV and
that of LUMO is -0.099 eV. The energy gap between them is -0.12 eV, which shows the
possibility of flow of energy from HOMO to LUMO. The electro negativity is a measure of
attraction for electrons in a covalent bond is found to be 0.021. The global hardness is a
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/216
Page 19
measure the resistance of an atom to charge transfer and it is found to be -0.141. The global
softness describes the capacity of an atom found to be 0.162. The electrophilicity index is a
measure total energy due to the maximal electron flow between the donors and the acceptors
and it is found to be -0.303 eV.
HOMO LUMO
Table. 7
Calculated energy value of the 3-Formyl-2-thienylboronic acid
by B3LYP/6-311++G(d,p) method.
Parameters values
EHOMO (eV) -0.219
ELUMO (eV) -0.099
EHOMO-LUMO gap (eV) -0.12
Electronegativity (χ) (eV) 0.021
Chemical hardness (η)
(eV)
-0.141
Global softness (ζ) (eV) 0.162
Electrophilicity index (ω)
(eV)
-0.303
MEP Analysis
In the present study, a 3D plot of molecular electrostatic potential (MEP) map of title
molecule is illustrated in Fig.6. The MEP which is a plot of electrostatic potential mapped the
electron density on the surface of the molecule. The importance of MEP lies in the fact that it
simultaneously displays molecular size, shape as well as positive, negative and neutral
Fig.9. HOMO and LUMO structure of 3-Formyl-2-thienylboronic acid
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/217
Page 20
electrostatic potential regions in terms of colour grading. The MEP is also useful to locate
and study the reactive regions of the molecule, the region where positive charges are found in
abundance are said to be electrophilic region as they can attach the electrons and cause
reactions. Similarly the regions which are rich in negative charges are said to be
Nucleophilic, as they can attract positive charges and cause reactions between molecules. In
the majority of the MEPs, the maximum negative regions are marked red in colour, while the
positive region are blue in colour [22].
Potential increases in the order red < orange < yellow < green < blue. The color code
of these maps is in the range between -5.27a.u. (deepest red) to 5.27a.u (deepest blue) in
compound. As can be seen from the MEP map of the title molecule, only the regions over the
three hydrogen atoms are positive and over three oxygen atoms are negative. The other
regions over the carbon atoms are closer to neutral.
Fig.12.MEP for 3-Formyl-2-thienylboronic acid
Conclusion:
The structural analysis show that the bond angles are considerable changed by
the presence of S and B atoms in the molecule, by changing the hybridisation of the carbon
atoms. The Bond lengths of the CC bonds within the thianyl ring show that there is
conjugation of electrons within the ring closer to that of benzene ring. This is also confirmed
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/218
Page 21
by the vibrational analysis; it also showed that no hydrogen bonding is possible with OH
groups of the boronic acid. The NMR chemical shifts indicate very high shift for all Carbon
atoms in the molecule due to the substitutional groups. The NBO analysis and UV-Vis
transitional analysis showed that S atom causes transition in the visible region due to n- π*
transition and all transitions which happen in the UV region are due to ζ to π* transitions in
the boronic acid group of the molecule.
Reference
[1] A.K. Sachan, S.K. Pathak, L.Sinha, O.Prasad, M. Karabacak et al., Journal of Molecular
structure volume 1075, 5 November 2014, 639-650.
[2] W. Tjarks, A.K.M. Anisuzzaman, L. Liu, S.H. Soloway, R.F. Barth, D.J. Perkins, D.M.
Adams, J. Med. Chem. 35 (1992) 16228–17861.
[3] A.H. Soloway, R.G. Fairchild, Sci. Am. 262 (1990) 100–107. Fig. 10. The temperature
dependence correlation graph of heat capacity, entropy, and enthalpy change. A.K. Sachan et
al. / Journal of Molecular Structure 1076 (2014) 639–650 649
[4] D.A. Matthews, R.A. Alden, J.J. Birktoft, S.T. Freer, J. Kraut, J. Biol. Chem. 250 (1975)
7120–7126.
[5] S.J. Rettig, J. Trotte, Can. J. Chem. 55 (1977) 3071–3075
[6] M.J. Frisch, et al., Gaussian 09 Program, Gaussian, Inc., Wallingford, CT, 2004.
[7] G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J.
Olson, AutoDock 4 and AutoDockTools 4: automated docking with selective receptor
flexibility, J. Comput. Chem. 30 (16) (2009) 2785e2791.
[8] S. Sangeetha margreat, S. Ramanlingam, S.Sabastian, S. Xavier ,S. Periandy et al., Journal
of Molecular Structure 1200 (2020)127099.
[9] Musiri M. Balakrishnarajan, Pattath D. Pancharatna and Roald Hoffmann journal of
chemistry Issue 4, 2007.
[10] P. S. Peek, D. P. Mcdermoot, Spectrochimica Acta 44 (1988) 371–377.
[11] D.L. Pavia, G.M. Lampman, G.S. Kriz, Introduction to Spectroscopy, third ed.,
Thomson Learning, Singapore, 2001. p. 52.
[12] J. D. Odom, P. A. Brletic, S. A. Johnston and J. R. Durig Journal of molecular structure
96 (1983)247-266.
[13] M. Sathish, S. Sebastian, S. Xavier ,S. Periandyet al., Journal of Molecular Structure 1164
(2018) 420e437
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/219
Page 22
[14] G. Shakilaa, S. Periandy, S. Ramalingam, Spectrochim. Acta 78A (2011)732e739.
[15] G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Hurey, W.E. Hart, R.K. Belew,A.J.
Olson, J. Comput. Chem. 19 (1998) 1639.
[16] R.M. Silverstein, G.C. Basster, T.C. Horrill, Spectrometric Identification of
Organic Compounds, fifth ed., John Wiley & Sons. Inc., New York, 1981.
[17] G.A. Jeffrey, J.R. Ruble, J.H. Yates, Acta Crystallogr. 39B (1983) 388–394.
[18] D. Sajan, J. Binoy, B. Pradeep, K.V. Krishnan, V.B. Kartha, I.H. Joe, V.S.
Jeyakumar, Spectrochim. Acta 60A (2004) 173–180.
[19] P. Perez, A. Toro-Labbe, A. Aizman, R. Contreras, Journal of Organic Chemistry,
67(2002) 4747.
[20] S. Ramalingam, S. Periandy, M. Karabacak, N. Karthikeyan, Molecular and
Biomolecular Spectroscopy 104 (2013) 337–351.
[21] N.M O’boyle, A.LTenderholt et al., J.comput. chem29(5)(2012)-580-592.
[22] R. Arathi, S Ramalingum and S Periandy et al., Journal of Acta Scientific
pharmaceutical science , January11, 2018.
ADALYA JOURNAL
Volume 9, Issue 1, January 2020
ISSN NO: 1301-2746
http://adalyajournal.com/220