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NMR, FT-IR, Raman and UV–Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid
Accepted Manuscript NMR, FT-IR, Raman and UV-Vis spectroscopic investigation and DFT study of 6Bromo-3-Pyridinyl Boronic Acid Gökhan Dikmen, Özgür Alver PII:
S0022-2860(15)00468-8
DOI:
10.1016/j.molstruc.2015.05.063
Reference:
MOLSTR 21618
To appear in:
Journal of Molecular Structure
Received Date: 29 January 2015 Revised Date:
13 May 2015
Accepted Date: 18 May 2015
Please cite this article as: G. Dikmen, Ö. Alver, NMR, FT-IR, Raman and UV-Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid, Journal of Molecular Structure (2015), doi: 10.1016/j.molstruc.2015.05.063. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
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Graphical Abstract
ACCEPTED MANUSCRIPT NMR, FT-IR, Raman and UV-Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid
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Gökhan Dikmena , Özgür Alverb,*
Central Research Laboratory, Osmangazi University, Eskisehir, Turkey
b
Department of Physics, Science Faculty, Anadolu University, Eskisehir, Turkey
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*
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Corresponding author: [email protected]
ACCEPTED MANUSCRIPT Abstract Possible stable conformers and geometrical molecular structures of 6-Bromo-3-Pyridinyl Boronic acid (6B3PBA; C5H5BBrNO2) were studied experimentally and theoretically using FT-IR and Raman spectroscopic methods. FT-IR and Raman spectra were recorded in the
investigated further, using 1H,
13
C, 1H coupled
13
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region of 4000–400 cm-1 and 3700–400 cm-1, respectively. The structural properties were C, HETCOR, COSY and APT NMR
techniques. The optimized geometric structures were searched by Becke-3–Lee–Yang–Parr
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(B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. Vibrational wavenumbers of 6B3PBA were calculated whereby B3LYP density functional methods
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including 6-311++G(d, p), 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. The comparison of the experimentally and theoretically obtained results using mean absolute error and experimental versus calculated correlation coefficients for the vibrational wavenumbers indicates that B3LYP method with 6-311++G(d, p) gives more satisfactory results for
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predicting vibrational wavenumbers when compared to the 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. However, this method and none of the mentioned methods here seem suitable for the calculations of OH stretching modes, most likely because
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increasing unharmonicity in the high wave number region and possible intra and inter molecular interactions at OH edges lead some deviations between experimental and
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theoretical results. Moreover, reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated using scaled quantum mechanical (SQM) method.
Keywords: 6-Bromo-3-Pyridinyl Boronic acid, Infrared and Raman spectra, NMR spectra, Molecular structure, DFT.
ACCEPTED MANUSCRIPT 1. Introduction Compounds containing boronic acid and its derivatives have been the center of attention in recent years. Moreover, chemical interaction of boron atom with inorganic and organic molecules is a considerable subject of research from the experimental and theoretical
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viewpoints [1-3]. Boronic acid (BA) and its derivatives are very important in various fields; such as material science, supramolecular chemistry, analytical chemistry, medicine, biology, catalysis, organic synthesis and crystal engineering. Especially, boronic acid has been used for
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organic synthesis, medicinal chemistry, and carbohydrate sensor design and anti cancerogen
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agents [1, 4].
Vibrational and NMR spectroscopic techniques have been widely used to determine structural characterization of molecular systems together with DFT (Density Functional Theory) calculations. In order to determine the physical and chemical properties of any molecule, DFT
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is both a cost effective and reliable method. The DFT/B3LYP model exhibits good performance on vibrational frequencies and geometries of organic compounds [5-16]. In this work, the most stable conformers of 6B3PBA have been studied within the framework of
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DFT. The vibrational wavenumbers, nuclear magnetic shielding properties and some important structural parameters were examined. The results of the theoretical and
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spectroscopic studies are reported here.
2. Experimental
A commercial sample of 6B3PBA (95%) was purchased and used without further purification. All NMR spectra of the title molecule were recorded on a Bruker Avance II 500 NMR spectrometer at usual probe temperature. The operating frequencies were 500.13 MHz and 125.76 MHz for 1H and
13
C, respectively. All measurements were done using deuterated
ACCEPTED MANUSCRIPT dimethyl sulfoxide as solvent. FT-IR spectrum was recorded using Bruker Optics IFS66v/s FTIR spectrometer at a resolution of 2 cm-1. For FT-IR measurements KBr pellet technique was used. The Raman spectrum was collected with a Bruker Senterra Dispersive Raman microscope spectrometer using 532nm excitation from a 3B diode laser having 3 cm−1
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resolution in the spectral region of 3700–400cm−1. The UV-Vis absorption spectra of the title molecule were recorded in ethanol, methanol and water solutions with Shimadzu 2101 PC
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Spectrophotometer in the spectral region of 200-800 nm.
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3. Calculations
Conformers of 6B3PBA examined in this study were suggested considering the previously reported study (Fig. 1) [17]. Cis-cis (cc), trans-trans (tt), cis-trans (ct) and trans-cis (tc) configurations of the title molecule were examined using the B3LYP with 6-311++G(d, p),
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6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) different level of theories in the gas phase. No geometric restrictions were applied during the optimization procedure. After the optimization no imaginary frequencies were found. Following the optimization, trans-cis (tc)
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conformer belonging to C1 point group was found as the most stable one. As a result, all the
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experimental findings were compared to trans-cis geometry of the title molecule calculated with B3LYP/6-311++G(d, p). TED calculations were carried out by Scaled Quantum Mechanics (SQM) program [18, 19]. All other related calculations were done using Gaussian 09 program on a personal computer [20].
ACCEPTED MANUSCRIPT 4. Results and discussion 4.1 Geometrical Structures In order to find stable conformers of 6B3PBA, particularly in the point group of C1, various
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possible structures were examined with B3LYP/6-311++G(d,p) level of theory (Fig. 1). Among the optimized structures, trans-cis conformation belonging to C1 point group resulted in the lowest optimization energy. Therefore, all the experimental results including infrared,
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Raman wavenumbers were compared with trans-cis configuration. In addition to that, the calculated geometric parameters (bond lengths, bond and dihedral angles) were derived from
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trans-cis structure of the title molecule. Obtained geometric parameters were compared with previously reported studies [21-25] and there seems a remarkable agreement among the data. The carbon atoms of the indene fragment shows nearly a planar structure. Calculated dihedral angle of Br-C1-C2-C3 and H7-C3-C4-C5 are nearly 180o. B-O12 and B-O14 bond distances
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were calculated as 1.3654 Å and 1.3707 Å, respectively showing an agreement with the previously reported data of 1.378 Å, 1.362, 1.361 Å, 1.353 and 1.372 Å [21-24]. C4-B bond length was calculated as 1.5678 Å in compliance with the data of 1.579 Å, 1.568 Å and 1.571
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Å reported before [22, 23, 25]. Bond angles O-B-O and C3-C4-C5 were calculated as
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117.6306o and 115.9563o those of which were reported before as 116.3o .and 117.2o [22].
The relative energy differences are given in Table 1. Relative mole fraction of cc could be ignored because its relative energy difference compared to tc isomer is more than 4.0 kcal/mol. As for the tt, tc and ct following equations can be written for the mole fractions of individual conformers where a, b, c stand for tc, ct and tt, respectively:
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=
, =
and,
Na+Nb+Nc=1
=
1 1 + +
=
1 + +
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c forms, Na and Nb are mole fractions of conformers a, b and c.
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can be written, where KT1 and KT2 are conformational equilibrium constants between a, b and
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= ∆/ , R=1.987x10-3 kcal/mol K, T=298 K and ∆ = ∆ − ∆ [26].
Regarding the calculated free energies for the gas phase, the following mole fractions were obtained: Na = 0.72, Nb = 0.25, Nc = 0.03. Based on the calculations, the tc form is the most stable and the most abundant conformer in the gas phase. Since Na larger than Nb the
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approximate mode descriptions were determined considering tc conformer.
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4.2. NMR studies of 6B3PBA
C and 1H NMR chemical shift values were reported before [27] but no detailed assignments
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and discussions were provided for the title molecule. In
13
C NMR spectrum of the title
molecule (Fig. 2) at first glance five different carbon atoms are expected but four of them can be seen. Quadrupolar relaxation mechanism of times, leading to a very weak and broadened particularly directly bonded to
11
11
B nucleus, causes very short relaxation
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C NMR signals for the carbon atoms
B atoms [28-31]. For that reason C4 carbon atom could not
be resolved clearly. It is most probably the weak hump (denoted with asterisk in Fig. 2) appeared just near by the C2 carbon atom. In 1H NMR spectrum (Fig. 3), integration values seem to have an agreement with the number of hydrogen atoms. H8 is a doublet and H7 is
ACCEPTED MANUSCRIPT doublet of doublet and H9 is again a doublet but splitting is not much wide. The explanation of the peak patterns can be summed up as following: As can be clearly seen in COSY NMR spectrum (Fig. 4) H7 and H8 are neighbor hydrogen atoms on pyridine ring so they split each other with 3JHH = 7.92 Hz. Furthermore, H7 is also splitted by H9 and vice versa with JHH = 2.04 Hz. Proton coupled 13C NMR spectrum is given in Fig. 5. C2, C3 and C5 split into
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4
two lines due to directly bonded hydrogen atoms with 1JC2, H = 172.46, 1JC3, H = 164.78 and 1
JC5, H = 182.18 Hz, respectively. In addition to that, C3 and C5 are further splitted into two by
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H9 and H7, respectively, with 3JC3, H9 = 7.00 and 3JC5, H7 = 8.34. C1 as seen in Fig. 5, has a quartet, it is most likely caused by H7, and H9. This peak is not triplet since H7 and H9 do not
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have the same chemical environment due to nitrogen atom (N6). It is also worth to note that bromine and particularly nitrogen atoms lead to increase in C-H coupling values where they close to the related carbon atom. In HETCOR NMR spectrum (Fig. 6), C2→H8, C3→H7 and
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C5→H9 connections can clearly be seen.
4.3. Vibrational studies of 6B3PBA
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6B3PBA consists of 15 atoms and it has 39 normal vibrational modes so it is a member of C1
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point group with only identity (E) symmetry operation. Obtained experimental results were assigned to the theoretical results of C1 (tc) form of 6B3PBA Theoretical results of infrared and Raman wavenumbers together with experimental results of the title molecule were presented in Table 2. Experimental and calculated (IR and Raman) spectra of 6B3PBA were given in Figs. 7-8. Moreover, calculated IR and Raman spectra and vibrational assignments of 6B3PBA with 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets were given in Fig. S1 and Table S1-S4.
ACCEPTED MANUSCRIPT Raman scattering activities were converted to Raman intensities using the given equation [32, 33]:
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f(v' − v" )) S" I" = hcv" v" +(1 − exp (− ) 3 kT Here, ʋo is the laser exciting wavenumber (in this study, ʋo = 18797 cm−1), ʋi the vibrational wavenumber of the ith normal mode and Si is the Raman scattering activity of the normal
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mode ʋi, f is a optional normalization factor for all peak intensities. h, k, c and T are Planck
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and Boltzmann constants, speed of light and temperature respectively.
CH stretching vibrations experimentally/theoretically appeared at 3097 cm-1 (IR), 3097 cm-1 (R)/3105 cm-1, 3061 cm-1 (IR), 3062 cm-1 (R)/ 3079 cm-1, 3046 cm-1 (IR), 3047 cm-1 (R)/ 3019 cm-1. Those values are in agreement with previously performed works [10-12]. Related
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TED values can be seen in Table 2. CC stretching vibrations with percentage TED values given in parenthesis experimentally/theoretically were observed at 1581 cm-1(R) & 1586 cm1
(IR) /1592 cm-1 (50%), and 1551 cm-1(R) & 1555 cm-1(IR) /1553 cm-1 (68%). The bands at
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1463 cm-1, 1446 cm-1 (IR) and 1461 cm-1 (R) seem a mixed type of CC stretching and HCC bending vibrations with related TED values given in Table 2. In previously reported studies
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BO stretching modes were given between 1393-1310 cm-1 [8, 12]. In present study, BO stretching vibrations experimentally were observed at 1380 cm-1 (R)/1380 cm-1 (IR), 1346 cm1
(R)/1344 cm-1 (IR) and 1295 cm-1 (R)/1296 cm-1 (IR). Those values theoretically were found
as 1376 cm-1 (51%), 1349 cm-1 (13%) and 1303 cm-1 (19%).
In the literature, experimental/theoretical IR results for OH stretching vibrations of the boronic acid derivatives (in cm-1) were reported as 3889/3465, 3888/3449, 3887/3443,
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3854/3400,
3848/3449,
3847/3397,
3846/3397,
3846/3276,
3836/3257,
3847/3332, 3846/3425, 3834/3424, 3799/3249, 3789/3335, 3762/3467 [1, 13, 14, 16, 34, 35]. In present study there is a broad band around 3340 cm-1. In the Raman spectrum this band cannot be observed due to its low polarizability. As for the OH stretching mode, the big
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difference between the experimental and unscaled values can be explained in terms of increasing unharmonicity in the high wave number region, and the molecular interactions of the title molecule especially at the OH edges disturbing the electron density around these
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edges and leading expected shifts in the infrared spectrum.
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In order to make a comparison, following (IR/Raman) mean absolute error values for vibrational wavenumbers have been found for relative basis sets: 8.1/8.7, 10.1/10.3, 8.9/10.1, 9.7/8.8, 10.1/9.8 cm−1, (6-311++G(d,p), 6-311G(d,p), 6-311G(d), 6-31G(d,p) and 6-31G(d)). Furthermore, the correlation graphics based on the experimental-calculated wavenumbers were presented in Fig. S2. Based on the data obtained from mean absolute error and
experimental results.
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correlation values 6-311++G(d,p) basis sets seems to have better agreement with the
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In general, B3LYP/6-311++G(d,p) level of calculation with the dual scaling factors and SQM methodology provided good agreement with the experimental findings. From here, it can be
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conclude that B3LYP/6-311++G(d,p) method is reliable and it makes easier the understanding of vibrational spectrum and structural parameters of 6B3PBA and it provides more accurate data than the basis sets mentioned here.
ACCEPTED MANUSCRIPT 4.4. Electronic Properties 4.4.1. UV-VIS Spectrum UV-VIS experimental spectrum of 6B3PBA molecule was measured in water, ethanol and
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methanol at room temperature. In addition, theoretical UV-VIS spectrum and electronic transitions were obtained using B3LYP/6-311++G(d,p) method in the TD-DFT framework. TD-DFT calculations is a reasonable method to determine UV-VIS spectrum of any molecule
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and so, this method has been commonly used in literature. Moreover, these methods are computationally expensive according to semi empirical methods [36-39]. Theoretical
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wavelengths (λ), excitation energies (E), electronic transitions and experimental absorption wavelengths and energies are given in Table 3 in three solvents. Theoretical experiments were carried out for monomer structure of 6B3PBA molecule and this monomer structure was tc (trans-cis) form. In addition, both experimental and theoretical UV-VIS spectra of 6B3PBA
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molecule were shown in Fig. 9. Experimental values of maximum absorption are 219 and 267 nm in water, 224 and 267 nm in ethanol and 223 and 267 nm in methanol. Calculated values were assigned as 219 and 254 nm, 244 and 254 nm, 243 and 254 nm using TD-DFT-6-
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311++G(d, p) method in water, ethanol and methanol.
4.4.2. Frontier Molecular Orbital Analysis HOMO is described as highest occupied molecular orbital and LUMO is described as lowest unoccupied molecular orbital, determine the way the molecule interacts with other species, but in the same time both HOMO and LUMO are also called as FMOs which is frontier molecular orbital. Because, the ones occupy at the outermost boundaries of the electrons of any molecule. HOMO is related to ability of electron giving of a molecule, while LUMO is
ACCEPTED MANUSCRIPT related to ability of electron accepting. HOMO and LUMO are inform such as explains types of reaction, for predicting the most reactive position [40-43]. In order to find out the bonding scheme of 6B3PBA molecule the frontier orbitals FMOs such
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as H-1→L, H→L, H→L+1, H→L+2, H-1→L+1 and H-1→L+2 orbitals are shown Fig. S3. The nodes of HOMO orbital located on the ring and bromine atom. But, the nodes of LUMO located symmetrically all over the 6B3PBA molecule. In here, red color shows positive charge, while green color shows negative charge. Charge of bromine atom definitively shifted
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OH groups from HOMO to LUMO of title molecule. HOMO shows the π bonding character
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whereas LUMO indicates significant π anti bonding character [44]. Eventually FMOs energy gap clarifies charge transfer from HOMO to LUMO and charge transfer interactions in the molecule. HOMO and LUMO energy calculated by B3LYP/6-311++G(d,p) method for gas phase. The energy gap shows the eventual charge transfer interactions occurring in the
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molecule. The energy gap is that HOMOenergy (B3LYP) = -7.33 eV
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LUMOenergy (B3LYP) = -1.77 eV
(HOMO-LUMO)energy gap (B3LYP) = 5.56 eV
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The energy gaps for H-1→L, H→L, H→L+1, H→L+2, H-1→L+1 and H-1→L+2 were calculated as 6.02, 5.56, 5.86, 6.58, 6.32 and 7.04 eV respectively for 6B3PBA molecule (Table S4)
4.4.3. Molecular Electrostatic Potential Surface The MEP surface generally gives information about chemical reactivity of a molecule. Electrostatic potential which is occurred around a molecule is facilitate to understand amount
ACCEPTED MANUSCRIPT of electrophilic or nucleophilic molecular space [45]. MEP is related to electrostatic interaction energy of a molecule with a proton [46]. Nucleophilic attack symptoms are shown as blue color and this color shows maximum positive region, whereas electrophile attack symptoms are indicated as red color and it shows negative region. Concisely, the MEPs give a
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lot of information according to change of color such as molecular size, molecular shape, positive, negative and neutral electrostatic potential regions and thus we get information about
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physicochemical property of a molecule [47-48].
The MEPs of 6B3PBA molecule are shown in Fig. S5 as 2D and 3D. Electrostatic potential
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are demonstrated by different colors in the map of MEPs. In here, the potential value increases from red to blue color. The colors in the range from to in this compound. The blue is responsible for strongest attraction, while the other color is responsible for strongest
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repulsion.
The MEPs map of 6B3PBA showed that near OH groups have positive potential, while over the oxygen atoms (O12 and O14) have negative potential. Accordingly this results, near the H11
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and H13 atoms show the strongest attraction (because of blue color), O12 and O14 atoms show the strongest repulsion (because of green color). The 2D MEPs are represented in the
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molecular plane of the6B3PBA molecule. While the close surrounding of the oxygen atoms shows electron rich area the hydrogen atoms show electron deficient area. In addition, thermodynamic properties of tc form of 6B3PBA such as zero point vibrational energy, thermal energy, entropy and dipole moment are calculated at room temperature using B3LYP/6-311++G(d,p) method and shown in Table S6.
ACCEPTED MANUSCRIPT 5. Conclusion In this study experimental and theoretically Raman and IR spectra were analyzed using Gaussian 9.0 with B3LYP/6-311++G(d,p) level of theory. Among the calculated conformers
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trans-cis conformer was found having the lowest optimized energy in the gas phase. All the experimental vibrational bands have been discussed and assigned with TED values and some important structural parameters were also calculated using the same method. In general, there is good agreement between experimental and theoretically vibrations. Possible discrepancies
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between the experimental and theoretically calculated wave numbers, especially at the high
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wave number region, were attributed the unharmonicity of the vibrations and possible molecular interactions. It must be noted that theoretical calculations were done for a single isolated molecule that is not the case for experimental measurements. It is also worth to emphasize that as the basis sets getting larger such as from 6-31 G(d) to 6-31 G(d, p) and from 6-311 G(d) to 6-311 G(d, p), the deviations between experimental and calculated values
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of wavenumbers particularly for OH stretching mode tend to increase. If the assignments of experimental and theoretically calculated vibrational wavenumbers were carefully done based
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on the information in the literature or considering the nature of the band such as band width and intensity, then SQM method can be used to match both experimental and calculated
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values. In general, B3LYP/6-311++G(d, p) level of theory can be suggested to use for the investigation of vibrational and geometrical properties of the title molecule. However, it must be also noted that none of the basis sets used in this study resulted in good NMR results when compared to experimental NMR values. Henceforth, the theoretical NMR results did not discussed here and requires further investigations.
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Mol Model 19 (2013) 2015–2026.
[45] M. Karnan, V. Balachandran, M. Murugan, M.K. Murali, A. Natrj, Spectrochim. Acta A 116 (2013) 84-95.
[46] D.S. Kosov and P.L.A. Popelier, J. Phys. Chem. A 104 (2000) 7339-7345. [47] B.A. Christer, K.W. Tharanga, D. John, J. Mol. Struct. 1072 (2014) 20-27.
ACCEPTED MANUSCRIPT [48] M. Karabacak, E. Kose, E.B. Sas, M. Kurt, A.M. Asiri, A. Atac, Spectrochim. Acta A
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136(2015) 306-320.
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Tables Table 1. Calculated energy differences for three conformers of 6B3PBA by DFT (B3LYP/6311++G(d,p)) method. Table 2. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) of
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6B3PBA in gas phase.
Table 3. Experimental and calculated wavelengths (λ), excitation energies, of 6B3PBA in
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ethanol, methanol and water.
ACCEPTED MANUSCRIPT Table 1. Calculated energy differences for three conformers of 6B3PBA by DFT (B3LYP/6311++G(d,p)) method.
(kcal/mol)
-2997.98087630 -2997.97985772 -2997.97817345 -2997.97423567
-1881259.9817 -1881259.3425 -1881258.2856 -1881255.8147
Energy differences (Hartree) (kcal/mol) 0.00000 -0.00102 -0.00270 -0.00664
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Trans-cis (tc) Cis-trans (ct) Trans-trans (tt) Cis-cis (cc)
(Hartree)
0.00 -0.64 -1.69 -4.17
Dipole Moment (Debye) 2.6601 4.1032 5.8541 1.9549
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Energy Conformers
ACCEPTED MANUSCRIPT Table 2. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ23 υ24 υ25 υ26 υ27
Raman
3340 3097 3061 3046 1586 1555 1463 1380 1344 1296 1234 1177 1134 1088 1057 1030 937
3097 3062 3047 1581 1551 1461 1380 1346 1295 1234 1175 1090 -
M AN U
υ19 υ20 υ21 υ22
υ13-12(100) υ8-2(91) υ7-3(91) υ9-5(100) υ3-2(27) + υ4-3(12) + υ15-14(11) + υ5-4(11) υ2-1(26) + υ4-3(24) + υ5-4(18) + υ6-1(10) υ15-4 (25) + υ3-2(20) υ15-12(26) + υ15-14(25) υ15-12(13) + υ15-4(11) + δ3-2-8(11) + δ7-3-2(11) υ15-14(19) + υ6-5(16) + υ15-12(12) + υ4-3(10) υ6-1(27) + υ6-5(24) + υ5-4(15) + υ2-1(14) δ6-5-9(21) + δ9-5-4(20) + δ8-2-1(14) + δ3-2-8(12) δ7-3-2(25) + υ3-2(22) + δ4-3-7(20) υ4-3(15) + δ9-5-4(15) + δ6-5-9(13) δ6-5-9(13) + υ6-1(10) υ6-1(18) + δ13-12-15(11) + δ8-2-1(10) δ15-14-11(67) + υ15-12(20) τ4-3-2-8(23) + τ8-2-1-10(20) + τ15-4-3-7(13) + τ7-3-2-1(13) + τ8-2-1-6(12) δ2-1-6(14) + υ15-4(11) τ5-6-1-2(14) + τ3-2-1-6(14) + τ1-6-5-4(10) τ14-15-12-13(25) + τ14-15-4-5(13) + τ12-15-4-3(12) δ1-6-5(20) + δ6-5-4(15) + δ4-3-2(14) + δ3-2-1(14) δ12-15-14(16) + υ15-4(15) + υ10-1(12) + δ5-4-3(10) τ12-15-14-11(24) + τ4-15-12-13(14) τ4-15-14-11(32) + τ12-15-14-11(22) δ4-15-12(27) + δ4-15-14(22) + δ5-4-15(14) + δ15-4-3(13) δ12-15-14(34) + υ10-1(29) + δ4-5-14(11)
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υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9 υ10 υ11 υ12 υ13 υ14 υ15 υ16 υ17 υ18
IR
B3LYP / 6-311++G(d,p) Unscaled SQM IIR Freq. 3887 3340 22.32 3212 3105 0.16 3186 3079 0.23 3124 3019 9.11 1614 1592 51.25 1580 1553 12.53 1494 1464 7.97 1411 1376 48.97 1369 1349 100.00 1357 1303 37.59 1326 1236 5.47 1276 1171 4.10 1158 1130 1.60 1138 1089 34.62 1092 1061 20.50 1019 1013 41.23 979 942 27.79
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Assignments
SC
Mode
EP
21.06 14.04 21.38 52.81 3.37 2.56 0.84 23.82 4.74 3.89 1.62 1.10 -
841 803 740 665
774 650
853 778 758 672
838 779 738 658
3.19 8.20 4.10 15.49
29.16 0.09
611
591 -
642
631
0.68
10.44
549 474 458
474 441
567 472 451
571 461 442
5.47 22.55 15.72
1.56 1.08
422 404
429 404
431 401
430 398
0.91 1.37
2.78 0.58
IR: Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ, δ, τ: stretching, bending and torsion, respectively.
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ACCEPTED MANUSCRIPT Table 3. Experimental and calculated wavelengths (λ), excitation energies, of 6B3PBA in ethanol, methanol and water.
5.0906 In Methanol 243 5.0941 254 4.8850
H→L (64%), H→L+1 (24%), H-3→L (6%), H-3→L+1 (4%) H→L (64%), H-2→L+1 (2%)
224
5.5350
267
4.6436
π→π* π→π*
H-1→L+1 (97%), H-2→L+1 (2%) H→L (64%), H→L+1 (24%), H-3→L (6%), H-3→L+1 (4%)
223 267
5.5598 4.6436
π→π* π→π*
H→L+2 (94%), H→L+3 (4%) H→L (64%), H→L+1 (24%), H-3→L (6%), H-3→L+1 (4%)
219 267
5.6614 4.6436
π→π*
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In Water 219 5.6599 254 4.8857
λ (nm) E (eV) Experimental
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254
Major contributes
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λ (nm) E (eV) Assignments B3LYP/6-311++G(d, p) In Ethanol 244 4.8119 π→π*
ACCEPTED MANUSCRIPT Figures Figure 1. Possible conformers of 6B3PBA. Figure 2. 13C NMR spectrum of 6B3PBA.
Figure 4. COSY NMR spectrum of 6B3PBA. Figure 5. 1H coupled 13C NMR spectrum of 6B3PBA. Figure 6. HETCOR NMR spectrum of 6B3PBA.
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Figure 3. 1H NMR spectrum of 6B3PBA.
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Figure 7. Experimental (A) and scaled calculated (B) Infrared spectrum of 6B3PBA. Figure 8. Experimental (A) and scaled calculated (B) Raman spectrum of 6B3PBA.
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Figure 9. Experimental and theoretical UV-VIS spectra of 6B3PBA in water, ethanol and
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methanol.
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cis-cis (cc)
trans-trans (tt)
SC
Trans-cis (tc)
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Figure 1. Possible conformers of 6B3PB
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Figure 1. Possible conformers of 6B3PBA.
cis-trans (ct)
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Figure 2. 13C NMR spectrum of 6B3PBA.
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Figure 3. 1H NMR spectrum of 6B3PBA.
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Figure 4. COSY NMR spectrum of 6B3PBA.
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Figure 5. 1H coupled 13C NMR spectrum of 6B3PBA.
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Figure 6. HETCOR NMR spectrum of 6B3PBA.
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Figure 7. Experimental (A) and scaled calculated (B) Infrared spectrum of 6B3PBA.
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Figure 8. Experimental (A) and scaled calculated (B) Raman spectrum of 6B3PBA.
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Figure 9. Experimental and theoretical UV-VIS spectra of 6B3PBA in water, ethanol and methanol.
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NMR study
UV-Vis study
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DFT study of 6-Bromo-3-Pyridinyl Boronic Acid
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FT-IR and Raman studies
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Supplementary Figures Figure S1. Theoretical IR and Raman spectra in different bases sets. Figure S2. Plot of the experimental and theoretical vibrational frequencies of 6B3PBA
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molecule. Figure S3. Atomic orbital compositions of the frontier molecular orbital for 6B3PBA.
Figure S4. The molecular electrostatic potential 3D map and 2D counter map for 6B3PBA
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molecule.
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Figure S1. Theoretical IR and Raman spectra in different base sets.
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Figure S2. Plot of the experimental and theoretical vibrational frequencies of 6B3PBA molecule.
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Figure S2. (continued)
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Figure S3. Atomic orbital compositions of the frontier molecular orbital for 6B3PBA.
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Figure S4. The molecular electrostatic potential 3D map (A) and 2D counter map (B) for 6B3PBA molecule.
ACCEPTED MANUSCRIPT Supplementary Tables Table S1. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-311G(d, p) method) of 6B3PBA in gas phase.
(B3LYP/6-311G(d) method) of 6B3PBA in gas phase.
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Table S2. Comparison of the experimental and calculated vibrational wavenumbers (cm-1)
(B3LYP/6-31G(d, p) method) of 6B3PBA in gas phase.
SC
Table S3. Comparison of the experimental and calculated vibrational wavenumbers (cm-1)
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Table S4. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-31G(d) method) of 6B3PBA in gas phase.
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Table S5. The calculated energy values and the energy gaps of 6B3PBA molecule.
ACCEPTED MANUSCRIPT Table S1. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-311G(d,p) method) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ23 υ24 υ25 υ26 υ27
IR
Raman
3340 3097 3061 3046 1586 1555 1463 1380 1344 1296 1234 1177 1134 1088 1057 1030 937
3097 3062 3047 1581 1551 1461 1380 1346 1295 1234 1175 1090 -
841 803 740 665
774 650
840 761 747 657
845 772 739 657
3.37 9.46 4.49 17.09
25.45 0.51
611
591
627
626
0.76
9.53
549 474
474
555 465
566 465
5.57 25.81
1.20
458
441
445
444
11.48
2.32
422 404
429 404
422 393
424 396
0.79 1.10
2.38 1.01
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υ19 υ20 υ21 υ22
υ13-12(100) υ8-2(91) υ7-3(91) υ9-5(100) υ3-2(28) + υ5-4(13) + υ4-3(11) + υ15-4(10) υ4-3(27) + υ2-1(26) + υ5-4(16) υ15-4 (22) + υ3-2(22) + υ5-4(10) υ15-14(26) + υ15-12(15) + υ2-1(10) υ15-12(25) + υ15-4(11) υ15-14(22) + υ4-3(12) + υ6-5(10) + υ15-12(10) υ2-1(21) + δ6-5-9(20) + υ6-1(14) + δ9-5-4(10) υ6-5(27) + δ6-5-9(17) + δ9-5-4(14) + υ6-1(13) υ3-2(28) + δ7-3-2(20) + δ4-3-7(15) υ4-3(15) + δ13-12-15 (14) + δ6-5-9(10) υ6-5(10) + υ10-1(10) υ6-1(18) + δ13-12-15(11) + δ8-2-1(10) δ15-14-11(42) + υ15-12(26) + υ15-14(11) τ4-3-2-8(23) + τ8-2-1-10(21) + τ15-4-3-7(13) + τ8-2-1-6(13) + τ7-3-2-1(12) δ2-1-6(14) + υ15-4(11) τ5-6-1-2(15) + τ3-2-1-6(14) + τ1-6-5-4(10) τ14-15-12-13(30)+τ14-15-4-5(12)+τ12-15-4-3(12) δ1-6-5(21) + δ6-5-4(15) + δ4-3-2(14) + δ3-2-1(14) δ12-15-14(16) + υ15-4(15) + υ10-1(13) + δ5-4-3(10) τ12-15-14-11(34) + τ4-15-12-13(13) τ4-15-14-11(26) + τ12-15-14-11(14) + τ5-4-3-2(10) δ4-15-12(27) + δ4-15-14(22) + δ5-4-15(14) + δ15-4-3(13) δ12-15-14(34) + υ10-1(29) + δ4-15-14(11)
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υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9 υ10 υ11 υ12 υ13 υ14 υ15 υ16 υ17 υ18
B3LYP / 6-311G(d,p) Scaled SQM IIR Freq. 3672 3340 20.88 3068 3106 0.31 3044 3081 0.32 2980 3016 10.52 1579 1593 50.25 1548 1557 13.22 1461 1460 9.11 1394 1372 49.48 1344 1351 100 1330 1297 29.49 1298 1221 4.26 1249 1181 3.26 1131 1135 1.45 1115 1103 31.12 1068 1051 24.38 1003 1008 37.17 967 951 30.30
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Assignments
SC
Mode
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EP
Scaled with 0.955 above 1800cm−1, 0.977 under 1800cm−1. IR:Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ,δ,τ: stretching, bending and torsion, respectively.
IR 19.95 13.68 22.02 47.83 2.64 1.77 0.83 20.16 4.11 2.83 1.76 0.72 -
ACCEPTED MANUSCRIPT Table S2. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-311G(d) method) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ23 υ24 υ25 υ26 υ27
Raman
3340 3097 3061 3046 1586 1555 1463 1380 1344 1296 1234
3097 3062 3047 1581 1551 1461 1380 1346 1295 1234
1177 1134 1088 1057 1030 937
1175 1090 -
841 803 740 665
B3LYP / 6-311G(d) SQM IIR 14.05 0.78 0.49 12.67 50.72 13.36 10.07 50.47 100 35.03 4.79
20.09 12.96 21.42 47.61 2.44 1.32 0.88 19.66 4.26 3.24
1250 1136 1118 1069 1007 967
1173 1136 1104 1049 1009 949
3.43 1.34 33.75 24.86 33.22 32.60
1.61 0.64 -
774 650
836 761 747 664
838 770 735 661
3.65 9.82 4.90 22.37
25.50 0.48
611
591
628
629
0.80
9.58
549
-
553
564
6.31
-
474 458
474 441
473 451
472 447
38.36 5.20
1.48 1.90
422 404
429 404
421 396
424 394
0.98 0.75
2.52 0.94
Scaled with 0.955 above 1800cm−1, 0.977 under 1800cm−1. IR:Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ,δ,τ: stretching, bending and torsion, respectively.
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IR
3340 3105 3082 3015 1594 1556 1459 1374 1353 1297 1229
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υ19 υ20 υ21 υ22
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υ13 υ14 υ15 υ16 υ17 υ18
υ13-12(100) υ8-2(89) + υ7-3(11) υ7-3(89) + υ8-2(11) υ9-5(100) υ3-2(27) + υ5-4(13) + υ4-3(10) + υ15-4(10) υ2-1(26) + υ4-3(27) + υ5-4(15) υ15-4 (21) + υ3-2(23) + υ5-4(11) υ15-12(11) + υ15-14(26) υ15-12(31) + υ15-4(10) υ15-14(21) + υ4-3(13) + δ9-5-4(13) υ2-1(23) + δ8-2-1(12) + δ9-5-4(16) + δ6-5-9(21) δ7-3-2(11) + δ4-3-7(12) + υ5-4(15) + υ6-1(14) + υ6-5(23) δ7-3-2(12) + υ3-2(33) + δ3-2-8(10) υ4-3(14) + υ6-5(17) + δ13-12-15 (13) δ 6-5-4(10) + υ6-5(10) δ13-12-15(59) + δ15-14-11(10) + υ15-14(16) δ15-14-11(37) + υ15-12(25) + υ15-14(12) τ4-3-2-8(23) + τ8-2-1-10(20) + τ15-4-3-7(13) + τ7-3-2-1(12) + τ8-2-1-6(13) δ2-1-6(14) + υ15-4(11) τ5-6-1-2(15) + τ3-2-1-6(14) + τ1-6-5-4(10) τ14-15-12-13(36)+τ14-15-4-5(11)+τ12-15-4-3(11) δ1-6-5(21) + δ6-5-4(15) + δ4-3-2(14) + δ3-2-1(14) δ12-15-14(16) + υ15-4(16) + υ10-1(13) + δ5-4-3(10) τ12-15-14-11(20) + τ4-15-12-13(11) + τ12-15-14-11(45) τ4-15-14-11(17) + τ5-4-3-2(11) δ4-15-12(27) + δ4-15-14(22) + δ5-4-15(15) + δ15-4-3(13) δ12-15-14(34) + υ10-1(28) + δ4-15-14(12)
EP
υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9 υ10 υ11 υ12
IR
Scaled Freq. 3638 3071 3048 2982 1584 1551 1468 1396 1348 1335 1304
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Assignments
SC
Mode
ACCEPTED MANUSCRIPT Table S3. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-31G(d,p) method) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ15 υ16 υ17 υ18 υ19 υ20 υ21 υ22 υ23 υ24 υ25 υ26 υ27
Raman
3340 3097 3061 3046 1586 1555 1463 1380
3097 3062 3047 1581 1551 1461 1380
1344 1296 1234
1346 1295 1234
1177 1134
1175 -
B3LYP / 6-31G(d,p) SQM IIR 20.24 0.38 0.48 14.06 57.93 15.18 9.19 60.02
18.22 13.35 20.56 49.99 1.77 1.41 1.14
1357 1341 1307
1350 1299 1240
100 53.90 3.80
18.47 7.06 2.82
1271 1136
1172 1131
3.13 2.07
-
1.49
1088 1057 1030 937
1090 -
1120 1076 1001 969
1092 1056 1011 943
36.33 25.14 45.58 37.77
1.56 -
841 803 740 665
774 650
843 760 748 644
846 771 744 645
3.54 11.14 3.21 19.30
23.94 0.35
611
591
626
629
1.02
9.63
549 474 458
474 441
556 467 448
567 467 448
6.33 26.74 19.33
2.47 3.12
422
429
423
430
0.84
2.42
404
404
396
399
2.04
0.81
Scaled with 0.955 above 1800cm−1, 0.977 under 1800cm−1. IR:Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ,δ,τ: stretching, bending and torsion, respectively.
AC C
IR
3340 3108 3082 3012 1593 1553 1461 1376
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υ13 υ14
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υ10 υ11 υ12
υ13-12(100) υ8-2(92) υ7-3(93) υ9-5(100) υ3-2(28) + υ4-3(13) + υ15-4(10) + υ5-4(11) υ2-1(27) + υ4-3(24) + υ5-4(17) υ15-4 (23) + υ3-2(20) υ15-12(22) + υ15-14(23) + υ2-1(10) υ15-12(15) + υ15-4(12) + δ3-2-8(10) + δ7-3-2(10) υ15-14(21) + υ6-5(15) + υ15-12(13) + υ4-3(10) υ6-1(26) + υ6-5(23) + υ5-4(15) + υ2-1(15) δ6-5-9(21) + δ9-5-4(20) + υ6-5(10) + δ8-2-1(14) + δ3-2-8(12) δ7-3-2(25) + υ3-2(23) + δ4-3-7(19) υ4-3(14) + δ9-5-4(14) + δ6-5-9(14) + δ13-12-15 (12) υ6-5(10) + υ6-1(11) + δ6-5-9(11) υ6-1(17) + δ13-12-15(19) δ15-14-11(48) + υ15-12(25) + υ15-14(10) τ4-3-2-8(23) + τ8-2-1-10(22) + τ15-4-3-7(12) + τ7-3-2-1(13) + τ8-2-1-6(12) δ2-1-6(14) + υ15-4(10) τ5-6-1-2(16) + τ3-2-1-6(15) + τ1-6-5-4(11) τ14-15-12-13(30)+τ14-15-4-5(14)+τ12-15-4-3(13) δ1-6-5(20) + δ6-5-4(15) + δ4-3-2(14) + δ3-21(14) δ12-15-14(17) + υ15-4(14) + υ10-1(12) + δ5-4-3(10) τ12-15-14-11(26) + τ4-15-12-13(15) τ4-15-14-11(32) + τ12-15-14-11(21) δ4-15-12(26) + δ4-15-14(23) + δ5-4-15(14) + δ15-4-3(12) δ12-15-14(33) + υ10-1(29) + δ4-15-14(10) + υ15-4(10)
EP
υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9
IR
Scaled Freq. 3437 3087 3061 2990 1595 1560 1473 1414
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Assignments
SC
Mode
ACCEPTED MANUSCRIPT Table S4. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-31G(d) method) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ19 υ20 υ21 υ22 υ23 υ24 υ25 υ26 υ27
Raman
3340 3097 3061 3046 1586 1555 1463 1380 1344 1296 1234
3097 3062 3047 1581 1551 1461 1380 1346 1295 1234
1177 1134
1175 -
1088 1057 1030 937
B3LYP / 6-31G(d) SQM IIR 19.67 0.53 0.58 15.53 59.56 15.41 10.60 61.86 100 61.36 4.17
18.18 13.01 20.27 50.31 1.71 21.38 1.07 18.22 7.49 3.06
1272 1142
1176 1139
3.33 1.77
1.36 -
1090 -
1124 1077 1006 974
1100 1048 1010 947
39.44 26.97 39.47 36.96
1.18 -
841 803 740 665
774 650
843 760 748 645
844 767 743 645
3.93 11.55 3.34 20.94
21.28 0.58
611
591
627
626
1.05
9.61
549
-
555
564
6.62
-
474 458
474 441
471 452
470 451
36.96 13.43
2.35 2.75
422 404
429 404
423 398
426 397
0.90 1.39
2.46 0.87
Scaled with 0.955 above 1800cm−1, 0.977 under 1800cm−1. IR:Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ,δ,τ: stretching, bending and torsion, respectively.
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IR
3340 3107 3082 3013 1595 1557 1460 1375 1352 1297 1227
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υ15 υ16 υ17 υ18
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υ13 υ14
υ13-12(100) υ8-2(91) υ7-3(91) υ9-5(100) υ3-2(27) + υ4-3(13) + υ15-4(10) + υ5-4(11) υ2-1(28) + υ4-3(24) + υ5-4(16) υ15-4 (22) + υ3-2(21) + υ5-4(11) υ15-12(10) + υ15-14(23) + υ2-1(10) υ15-12(26) + υ15-4(10) υ15-14(24) + υ6-5(10) + υ15-12(13) + υ4-3(11) υ6-1(19) + υ6-5(17) + υ5-4(13) + υ2-1(19) δ6-5-9(17) + δ9-5-4(18) + υ6-5(10) + δ8-2-1(14) + δ3-2-8(14) + υ6-5(16) δ7-3-2(21) + υ3-2(24) + δ4-3-7(15) υ4-3(15) + δ9-5-4(14) + δ6-5-9(14) + δ13-12-15 (12) + δ15-14-11(11) υ6-5(10) υ6-1(12) + δ13-12-15(45) δ15-14-11(35) + υ15-12(26) + υ15-14(14) τ4-3-2-8(23) + τ8-2-1-10(21) + τ15-4-3-7(13) + τ7-3-2-1(13) + τ8-2-1-6(12) δ2-1-6(14) + υ15-4(10) τ5-6-1-2(16) + τ3-2-1-6(15) + τ1-6-5-4(11) τ14-15-12-13(32)+τ14-15-4-5(13)+τ12-15-4-3(13) δ1-6-5(21) + δ6-5-4(15) + δ4-3-2(14) + δ3-2-1(14) δ12-15-14(16) + υ15-4(15) + υ10-1(12) + δ5-4-3(10) τ12-15-14-11(36) + τ4-15-12-13(14) + τ4-15-14-11(12) τ4-15-14-11(26) + τ12-15-14-11(13) δ4-15-12(23) + δ4-15-14(26) + δ5-4-15(14) + δ15-4-3(13) δ12-15-14(33) + υ10-1(29) + δ4-15-14(10)
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υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9 υ10 υ11 υ12
IR
Scaled Freq. 3599 3092 3068 2999 1598 1562 1479 1413 1358 1346 1313
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Assignments
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Mode
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EHOMO (eV) ELUMO (eV) EHOMO-1 (eV) ELUMO+1 (eV) ELUMO+2 (eV) EHOMO-LUMO (eV) EHOMO-1-LUMO (eV) EHOMO-LUMO+1 (eV) EHOMO-1-LUMO+1 (eV) EHOMO-LUMO+2 (eV) EHOMO-1-LUMO+2 (eV)
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Monomer (in gas phase) -7.33 -1.77 -7.79 -1.47 0.75 5.56 6.02 5.86 6.32 6.58 7.04
B3LYP/ 6-311++G(d,p)
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Table S5. The calculated energy values and the energy gaps of 6B3PBA molecule.
S0022-2860(15)00468-8
DOI:
10.1016/j.molstruc.2015.05.063
Reference:
MOLSTR 21618
To appear in:
Journal of Molecular Structure
Received Date: 29 January 2015 Revised Date:
13 May 2015
Accepted Date: 18 May 2015
Please cite this article as: G. Dikmen, Ö. Alver, NMR, FT-IR, Raman and UV-Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid, Journal of Molecular Structure (2015), doi: 10.1016/j.molstruc.2015.05.063. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
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Graphical Abstract
ACCEPTED MANUSCRIPT NMR, FT-IR, Raman and UV-Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid
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Gökhan Dikmena , Özgür Alverb,*
Central Research Laboratory, Osmangazi University, Eskisehir, Turkey
b
Department of Physics, Science Faculty, Anadolu University, Eskisehir, Turkey
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a
*
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Corresponding author: [email protected]
ACCEPTED MANUSCRIPT Abstract Possible stable conformers and geometrical molecular structures of 6-Bromo-3-Pyridinyl Boronic acid (6B3PBA; C5H5BBrNO2) were studied experimentally and theoretically using FT-IR and Raman spectroscopic methods. FT-IR and Raman spectra were recorded in the
investigated further, using 1H,
13
C, 1H coupled
13
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region of 4000–400 cm-1 and 3700–400 cm-1, respectively. The structural properties were C, HETCOR, COSY and APT NMR
techniques. The optimized geometric structures were searched by Becke-3–Lee–Yang–Parr
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(B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. Vibrational wavenumbers of 6B3PBA were calculated whereby B3LYP density functional methods
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including 6-311++G(d, p), 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. The comparison of the experimentally and theoretically obtained results using mean absolute error and experimental versus calculated correlation coefficients for the vibrational wavenumbers indicates that B3LYP method with 6-311++G(d, p) gives more satisfactory results for
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predicting vibrational wavenumbers when compared to the 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. However, this method and none of the mentioned methods here seem suitable for the calculations of OH stretching modes, most likely because
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increasing unharmonicity in the high wave number region and possible intra and inter molecular interactions at OH edges lead some deviations between experimental and
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theoretical results. Moreover, reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated using scaled quantum mechanical (SQM) method.
Keywords: 6-Bromo-3-Pyridinyl Boronic acid, Infrared and Raman spectra, NMR spectra, Molecular structure, DFT.
ACCEPTED MANUSCRIPT 1. Introduction Compounds containing boronic acid and its derivatives have been the center of attention in recent years. Moreover, chemical interaction of boron atom with inorganic and organic molecules is a considerable subject of research from the experimental and theoretical
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viewpoints [1-3]. Boronic acid (BA) and its derivatives are very important in various fields; such as material science, supramolecular chemistry, analytical chemistry, medicine, biology, catalysis, organic synthesis and crystal engineering. Especially, boronic acid has been used for
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organic synthesis, medicinal chemistry, and carbohydrate sensor design and anti cancerogen
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agents [1, 4].
Vibrational and NMR spectroscopic techniques have been widely used to determine structural characterization of molecular systems together with DFT (Density Functional Theory) calculations. In order to determine the physical and chemical properties of any molecule, DFT
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is both a cost effective and reliable method. The DFT/B3LYP model exhibits good performance on vibrational frequencies and geometries of organic compounds [5-16]. In this work, the most stable conformers of 6B3PBA have been studied within the framework of
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DFT. The vibrational wavenumbers, nuclear magnetic shielding properties and some important structural parameters were examined. The results of the theoretical and
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spectroscopic studies are reported here.
2. Experimental
A commercial sample of 6B3PBA (95%) was purchased and used without further purification. All NMR spectra of the title molecule were recorded on a Bruker Avance II 500 NMR spectrometer at usual probe temperature. The operating frequencies were 500.13 MHz and 125.76 MHz for 1H and
13
C, respectively. All measurements were done using deuterated
ACCEPTED MANUSCRIPT dimethyl sulfoxide as solvent. FT-IR spectrum was recorded using Bruker Optics IFS66v/s FTIR spectrometer at a resolution of 2 cm-1. For FT-IR measurements KBr pellet technique was used. The Raman spectrum was collected with a Bruker Senterra Dispersive Raman microscope spectrometer using 532nm excitation from a 3B diode laser having 3 cm−1
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resolution in the spectral region of 3700–400cm−1. The UV-Vis absorption spectra of the title molecule were recorded in ethanol, methanol and water solutions with Shimadzu 2101 PC
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Spectrophotometer in the spectral region of 200-800 nm.
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3. Calculations
Conformers of 6B3PBA examined in this study were suggested considering the previously reported study (Fig. 1) [17]. Cis-cis (cc), trans-trans (tt), cis-trans (ct) and trans-cis (tc) configurations of the title molecule were examined using the B3LYP with 6-311++G(d, p),
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6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) different level of theories in the gas phase. No geometric restrictions were applied during the optimization procedure. After the optimization no imaginary frequencies were found. Following the optimization, trans-cis (tc)
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conformer belonging to C1 point group was found as the most stable one. As a result, all the
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experimental findings were compared to trans-cis geometry of the title molecule calculated with B3LYP/6-311++G(d, p). TED calculations were carried out by Scaled Quantum Mechanics (SQM) program [18, 19]. All other related calculations were done using Gaussian 09 program on a personal computer [20].
ACCEPTED MANUSCRIPT 4. Results and discussion 4.1 Geometrical Structures In order to find stable conformers of 6B3PBA, particularly in the point group of C1, various
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possible structures were examined with B3LYP/6-311++G(d,p) level of theory (Fig. 1). Among the optimized structures, trans-cis conformation belonging to C1 point group resulted in the lowest optimization energy. Therefore, all the experimental results including infrared,
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Raman wavenumbers were compared with trans-cis configuration. In addition to that, the calculated geometric parameters (bond lengths, bond and dihedral angles) were derived from
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trans-cis structure of the title molecule. Obtained geometric parameters were compared with previously reported studies [21-25] and there seems a remarkable agreement among the data. The carbon atoms of the indene fragment shows nearly a planar structure. Calculated dihedral angle of Br-C1-C2-C3 and H7-C3-C4-C5 are nearly 180o. B-O12 and B-O14 bond distances
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were calculated as 1.3654 Å and 1.3707 Å, respectively showing an agreement with the previously reported data of 1.378 Å, 1.362, 1.361 Å, 1.353 and 1.372 Å [21-24]. C4-B bond length was calculated as 1.5678 Å in compliance with the data of 1.579 Å, 1.568 Å and 1.571
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Å reported before [22, 23, 25]. Bond angles O-B-O and C3-C4-C5 were calculated as
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117.6306o and 115.9563o those of which were reported before as 116.3o .and 117.2o [22].
The relative energy differences are given in Table 1. Relative mole fraction of cc could be ignored because its relative energy difference compared to tc isomer is more than 4.0 kcal/mol. As for the tt, tc and ct following equations can be written for the mole fractions of individual conformers where a, b, c stand for tc, ct and tt, respectively:
ACCEPTED MANUSCRIPT According to equilibrium given above:
=
, =
and,
Na+Nb+Nc=1
=
1 1 + +
=
1 + +
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c forms, Na and Nb are mole fractions of conformers a, b and c.
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can be written, where KT1 and KT2 are conformational equilibrium constants between a, b and
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= ∆/ , R=1.987x10-3 kcal/mol K, T=298 K and ∆ = ∆ − ∆ [26].
Regarding the calculated free energies for the gas phase, the following mole fractions were obtained: Na = 0.72, Nb = 0.25, Nc = 0.03. Based on the calculations, the tc form is the most stable and the most abundant conformer in the gas phase. Since Na larger than Nb the
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approximate mode descriptions were determined considering tc conformer.
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4.2. NMR studies of 6B3PBA
C and 1H NMR chemical shift values were reported before [27] but no detailed assignments
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and discussions were provided for the title molecule. In
13
C NMR spectrum of the title
molecule (Fig. 2) at first glance five different carbon atoms are expected but four of them can be seen. Quadrupolar relaxation mechanism of times, leading to a very weak and broadened particularly directly bonded to
11
11
B nucleus, causes very short relaxation
13
C NMR signals for the carbon atoms
B atoms [28-31]. For that reason C4 carbon atom could not
be resolved clearly. It is most probably the weak hump (denoted with asterisk in Fig. 2) appeared just near by the C2 carbon atom. In 1H NMR spectrum (Fig. 3), integration values seem to have an agreement with the number of hydrogen atoms. H8 is a doublet and H7 is
ACCEPTED MANUSCRIPT doublet of doublet and H9 is again a doublet but splitting is not much wide. The explanation of the peak patterns can be summed up as following: As can be clearly seen in COSY NMR spectrum (Fig. 4) H7 and H8 are neighbor hydrogen atoms on pyridine ring so they split each other with 3JHH = 7.92 Hz. Furthermore, H7 is also splitted by H9 and vice versa with JHH = 2.04 Hz. Proton coupled 13C NMR spectrum is given in Fig. 5. C2, C3 and C5 split into
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4
two lines due to directly bonded hydrogen atoms with 1JC2, H = 172.46, 1JC3, H = 164.78 and 1
JC5, H = 182.18 Hz, respectively. In addition to that, C3 and C5 are further splitted into two by
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H9 and H7, respectively, with 3JC3, H9 = 7.00 and 3JC5, H7 = 8.34. C1 as seen in Fig. 5, has a quartet, it is most likely caused by H7, and H9. This peak is not triplet since H7 and H9 do not
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have the same chemical environment due to nitrogen atom (N6). It is also worth to note that bromine and particularly nitrogen atoms lead to increase in C-H coupling values where they close to the related carbon atom. In HETCOR NMR spectrum (Fig. 6), C2→H8, C3→H7 and
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C5→H9 connections can clearly be seen.
4.3. Vibrational studies of 6B3PBA
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6B3PBA consists of 15 atoms and it has 39 normal vibrational modes so it is a member of C1
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point group with only identity (E) symmetry operation. Obtained experimental results were assigned to the theoretical results of C1 (tc) form of 6B3PBA Theoretical results of infrared and Raman wavenumbers together with experimental results of the title molecule were presented in Table 2. Experimental and calculated (IR and Raman) spectra of 6B3PBA were given in Figs. 7-8. Moreover, calculated IR and Raman spectra and vibrational assignments of 6B3PBA with 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets were given in Fig. S1 and Table S1-S4.
ACCEPTED MANUSCRIPT Raman scattering activities were converted to Raman intensities using the given equation [32, 33]:
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f(v' − v" )) S" I" = hcv" v" +(1 − exp (− ) 3 kT Here, ʋo is the laser exciting wavenumber (in this study, ʋo = 18797 cm−1), ʋi the vibrational wavenumber of the ith normal mode and Si is the Raman scattering activity of the normal
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mode ʋi, f is a optional normalization factor for all peak intensities. h, k, c and T are Planck
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and Boltzmann constants, speed of light and temperature respectively.
CH stretching vibrations experimentally/theoretically appeared at 3097 cm-1 (IR), 3097 cm-1 (R)/3105 cm-1, 3061 cm-1 (IR), 3062 cm-1 (R)/ 3079 cm-1, 3046 cm-1 (IR), 3047 cm-1 (R)/ 3019 cm-1. Those values are in agreement with previously performed works [10-12]. Related
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TED values can be seen in Table 2. CC stretching vibrations with percentage TED values given in parenthesis experimentally/theoretically were observed at 1581 cm-1(R) & 1586 cm1
(IR) /1592 cm-1 (50%), and 1551 cm-1(R) & 1555 cm-1(IR) /1553 cm-1 (68%). The bands at
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1463 cm-1, 1446 cm-1 (IR) and 1461 cm-1 (R) seem a mixed type of CC stretching and HCC bending vibrations with related TED values given in Table 2. In previously reported studies
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BO stretching modes were given between 1393-1310 cm-1 [8, 12]. In present study, BO stretching vibrations experimentally were observed at 1380 cm-1 (R)/1380 cm-1 (IR), 1346 cm1
(R)/1344 cm-1 (IR) and 1295 cm-1 (R)/1296 cm-1 (IR). Those values theoretically were found
as 1376 cm-1 (51%), 1349 cm-1 (13%) and 1303 cm-1 (19%).
In the literature, experimental/theoretical IR results for OH stretching vibrations of the boronic acid derivatives (in cm-1) were reported as 3889/3465, 3888/3449, 3887/3443,
ACCEPTED MANUSCRIPT 3881/3392,
3854/3400,
3848/3449,
3847/3397,
3846/3397,
3846/3276,
3836/3257,
3847/3332, 3846/3425, 3834/3424, 3799/3249, 3789/3335, 3762/3467 [1, 13, 14, 16, 34, 35]. In present study there is a broad band around 3340 cm-1. In the Raman spectrum this band cannot be observed due to its low polarizability. As for the OH stretching mode, the big
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difference between the experimental and unscaled values can be explained in terms of increasing unharmonicity in the high wave number region, and the molecular interactions of the title molecule especially at the OH edges disturbing the electron density around these
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edges and leading expected shifts in the infrared spectrum.
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In order to make a comparison, following (IR/Raman) mean absolute error values for vibrational wavenumbers have been found for relative basis sets: 8.1/8.7, 10.1/10.3, 8.9/10.1, 9.7/8.8, 10.1/9.8 cm−1, (6-311++G(d,p), 6-311G(d,p), 6-311G(d), 6-31G(d,p) and 6-31G(d)). Furthermore, the correlation graphics based on the experimental-calculated wavenumbers were presented in Fig. S2. Based on the data obtained from mean absolute error and
experimental results.
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correlation values 6-311++G(d,p) basis sets seems to have better agreement with the
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In general, B3LYP/6-311++G(d,p) level of calculation with the dual scaling factors and SQM methodology provided good agreement with the experimental findings. From here, it can be
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conclude that B3LYP/6-311++G(d,p) method is reliable and it makes easier the understanding of vibrational spectrum and structural parameters of 6B3PBA and it provides more accurate data than the basis sets mentioned here.
ACCEPTED MANUSCRIPT 4.4. Electronic Properties 4.4.1. UV-VIS Spectrum UV-VIS experimental spectrum of 6B3PBA molecule was measured in water, ethanol and
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methanol at room temperature. In addition, theoretical UV-VIS spectrum and electronic transitions were obtained using B3LYP/6-311++G(d,p) method in the TD-DFT framework. TD-DFT calculations is a reasonable method to determine UV-VIS spectrum of any molecule
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and so, this method has been commonly used in literature. Moreover, these methods are computationally expensive according to semi empirical methods [36-39]. Theoretical
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wavelengths (λ), excitation energies (E), electronic transitions and experimental absorption wavelengths and energies are given in Table 3 in three solvents. Theoretical experiments were carried out for monomer structure of 6B3PBA molecule and this monomer structure was tc (trans-cis) form. In addition, both experimental and theoretical UV-VIS spectra of 6B3PBA
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molecule were shown in Fig. 9. Experimental values of maximum absorption are 219 and 267 nm in water, 224 and 267 nm in ethanol and 223 and 267 nm in methanol. Calculated values were assigned as 219 and 254 nm, 244 and 254 nm, 243 and 254 nm using TD-DFT-6-
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311++G(d, p) method in water, ethanol and methanol.
4.4.2. Frontier Molecular Orbital Analysis HOMO is described as highest occupied molecular orbital and LUMO is described as lowest unoccupied molecular orbital, determine the way the molecule interacts with other species, but in the same time both HOMO and LUMO are also called as FMOs which is frontier molecular orbital. Because, the ones occupy at the outermost boundaries of the electrons of any molecule. HOMO is related to ability of electron giving of a molecule, while LUMO is
ACCEPTED MANUSCRIPT related to ability of electron accepting. HOMO and LUMO are inform such as explains types of reaction, for predicting the most reactive position [40-43]. In order to find out the bonding scheme of 6B3PBA molecule the frontier orbitals FMOs such
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as H-1→L, H→L, H→L+1, H→L+2, H-1→L+1 and H-1→L+2 orbitals are shown Fig. S3. The nodes of HOMO orbital located on the ring and bromine atom. But, the nodes of LUMO located symmetrically all over the 6B3PBA molecule. In here, red color shows positive charge, while green color shows negative charge. Charge of bromine atom definitively shifted
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OH groups from HOMO to LUMO of title molecule. HOMO shows the π bonding character
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whereas LUMO indicates significant π anti bonding character [44]. Eventually FMOs energy gap clarifies charge transfer from HOMO to LUMO and charge transfer interactions in the molecule. HOMO and LUMO energy calculated by B3LYP/6-311++G(d,p) method for gas phase. The energy gap shows the eventual charge transfer interactions occurring in the
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molecule. The energy gap is that HOMOenergy (B3LYP) = -7.33 eV
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LUMOenergy (B3LYP) = -1.77 eV
(HOMO-LUMO)energy gap (B3LYP) = 5.56 eV
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The energy gaps for H-1→L, H→L, H→L+1, H→L+2, H-1→L+1 and H-1→L+2 were calculated as 6.02, 5.56, 5.86, 6.58, 6.32 and 7.04 eV respectively for 6B3PBA molecule (Table S4)
4.4.3. Molecular Electrostatic Potential Surface The MEP surface generally gives information about chemical reactivity of a molecule. Electrostatic potential which is occurred around a molecule is facilitate to understand amount
ACCEPTED MANUSCRIPT of electrophilic or nucleophilic molecular space [45]. MEP is related to electrostatic interaction energy of a molecule with a proton [46]. Nucleophilic attack symptoms are shown as blue color and this color shows maximum positive region, whereas electrophile attack symptoms are indicated as red color and it shows negative region. Concisely, the MEPs give a
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lot of information according to change of color such as molecular size, molecular shape, positive, negative and neutral electrostatic potential regions and thus we get information about
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physicochemical property of a molecule [47-48].
The MEPs of 6B3PBA molecule are shown in Fig. S5 as 2D and 3D. Electrostatic potential
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are demonstrated by different colors in the map of MEPs. In here, the potential value increases from red to blue color. The colors in the range from to in this compound. The blue is responsible for strongest attraction, while the other color is responsible for strongest
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repulsion.
The MEPs map of 6B3PBA showed that near OH groups have positive potential, while over the oxygen atoms (O12 and O14) have negative potential. Accordingly this results, near the H11
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and H13 atoms show the strongest attraction (because of blue color), O12 and O14 atoms show the strongest repulsion (because of green color). The 2D MEPs are represented in the
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molecular plane of the6B3PBA molecule. While the close surrounding of the oxygen atoms shows electron rich area the hydrogen atoms show electron deficient area. In addition, thermodynamic properties of tc form of 6B3PBA such as zero point vibrational energy, thermal energy, entropy and dipole moment are calculated at room temperature using B3LYP/6-311++G(d,p) method and shown in Table S6.
ACCEPTED MANUSCRIPT 5. Conclusion In this study experimental and theoretically Raman and IR spectra were analyzed using Gaussian 9.0 with B3LYP/6-311++G(d,p) level of theory. Among the calculated conformers
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trans-cis conformer was found having the lowest optimized energy in the gas phase. All the experimental vibrational bands have been discussed and assigned with TED values and some important structural parameters were also calculated using the same method. In general, there is good agreement between experimental and theoretically vibrations. Possible discrepancies
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between the experimental and theoretically calculated wave numbers, especially at the high
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wave number region, were attributed the unharmonicity of the vibrations and possible molecular interactions. It must be noted that theoretical calculations were done for a single isolated molecule that is not the case for experimental measurements. It is also worth to emphasize that as the basis sets getting larger such as from 6-31 G(d) to 6-31 G(d, p) and from 6-311 G(d) to 6-311 G(d, p), the deviations between experimental and calculated values
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of wavenumbers particularly for OH stretching mode tend to increase. If the assignments of experimental and theoretically calculated vibrational wavenumbers were carefully done based
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on the information in the literature or considering the nature of the band such as band width and intensity, then SQM method can be used to match both experimental and calculated
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values. In general, B3LYP/6-311++G(d, p) level of theory can be suggested to use for the investigation of vibrational and geometrical properties of the title molecule. However, it must be also noted that none of the basis sets used in this study resulted in good NMR results when compared to experimental NMR values. Henceforth, the theoretical NMR results did not discussed here and requires further investigations.
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ACCEPTED MANUSCRIPT [19] J. Baker, A.A. Jarzecki, P. Pulay, J. Phys. Chem. A 102 (1998) 1412-1414. [20] M.J. Frisch et al. Gaussian 09, Revision A. 1, Gaussian, Inc, Wallingford, CT, 2009. [21] P. Rodriguez-Cuamatzi, H. Tlahuext, H. Höpfl, Acta Cryst. E65 (2009) o44–o45. [22] S.J. Rettig, J. Trotte, Can. J. Chem. 55 (1977) 3071–3075.
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[23] H.W.W. Ehrlich, Acta Cryst. 10 (1957) 699–705.
[24] M. Dabrowski, S. Lulinski, J. Serwatowski, Acta Cryst. E64 (2008) o437.
[25] P.N. Horton, M.B. Hursthouse, M.A. Becket, M.P.R. Hankey, Acta Cryst. E: Struct. Rep.
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E60 (2004) o2204- o2206.
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[27] P. R. Parry, C. Wang, A. S. Batsanov, M. R. Bryce, B. Tarbit, J. Org. Chem. 67 (2002) 7541-7543.
[28] R. A. Oliveira, R. O. Silva, G. A. Molander, P. H. Menezes, Magn. Reson. Chem. 47(10) (2009) 873-878.
1961, pp. 305 – 315.
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[29] A. Abragam, The Principles of Nuclear Magnetism, Oxford University Press, Oxford
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[30] V. Mlynarek, Progr. NMR Spectrosc. 18 (1986) 277-305. [31] B. Wrackmeyer, E. V. Klimkina, Z. Naturforsch, 63b (2008) 923-928.
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[32] G. Keresztury, S. Holly, J. Varga, G. Besenyei, A.Y. Wang, J.R. Durig, Spectrochim. Acta A 49A (1993) 2007-2026. [33] G. Keresztury, Raman spectroscopy: theory, in: J.M. Chalmers, P.R. Griffith (Eds.), Handbook of Vibrational Spectroscopy, Vol. 1, John Wiley & Sons Ltd., New York, 2002, pp. 71–87. [34] U. Rani, M. Karabacak, O. Tanrıverdi, M. Kurt, N. Sundaraganesand, Spectrochim. Acta A 92 (2012) 67-77 [35] M. Karabacak, L. Sinha, O. Prasad, A.M. Asiri, M. Çınar, Spectrochim. Acta A 115
ACCEPTED MANUSCRIPT (2013) 753–766. [36] A. Komal and M.K. Jitender, J. Mol. Struct. 1079 (2015) 21-34. [37] O. Mircea, C. Adrian, M. George, V. Mihai, I. Monica, L. Loredana, M. Dana, L. Nicolae, C. Vasile, Spectrochim. Acta A 97 (2012) 703–710.
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[38] C. Feifei, W. Yujiao, X. Xiaomei, C. Meng, L. Wei, Spectrochim. Acta A 128 (2014) 461–467.
[39]M. Karabacak, E. Kose, A. Atac, E.B. Sas, A.M. Asiri, M. Kurt, J. Mol. Struct. 1076
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(2014) 358-372.
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[40] P. Rajesh, S. Gunasekaran, T. Gnanasambandan, S. Seshadri, Spectrochim. Acta A 137 (2015) 1184–1193.
[41] M.C. Almandoz, M.I. Sancho, P.R. Duchowicz, S.E. Blanco, Spectrochim. Acta A 129 (2014) 52–60.
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[42] E.B. Sas, E. Kose, M. Kurt, M. Karabacak, Spectrochim. Acta A 137 (2015) 1315–1333. [43] A.K. Sachan, S.K. Pathak, L. Sinha, O. Prasad, M. Karabacak, A.M. Asiri, J. Mol. Struct.
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1076 (2014) 639-650.
[44] C.E. Maria, P.M. Judith, M.C.Victor, S.M. Guillermo, C. Margarita, M.J. Francisco, J
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Mol Model 19 (2013) 2015–2026.
[45] M. Karnan, V. Balachandran, M. Murugan, M.K. Murali, A. Natrj, Spectrochim. Acta A 116 (2013) 84-95.
[46] D.S. Kosov and P.L.A. Popelier, J. Phys. Chem. A 104 (2000) 7339-7345. [47] B.A. Christer, K.W. Tharanga, D. John, J. Mol. Struct. 1072 (2014) 20-27.
ACCEPTED MANUSCRIPT [48] M. Karabacak, E. Kose, E.B. Sas, M. Kurt, A.M. Asiri, A. Atac, Spectrochim. Acta A
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136(2015) 306-320.
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Tables Table 1. Calculated energy differences for three conformers of 6B3PBA by DFT (B3LYP/6311++G(d,p)) method. Table 2. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) of
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6B3PBA in gas phase.
Table 3. Experimental and calculated wavelengths (λ), excitation energies, of 6B3PBA in
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ethanol, methanol and water.
ACCEPTED MANUSCRIPT Table 1. Calculated energy differences for three conformers of 6B3PBA by DFT (B3LYP/6311++G(d,p)) method.
(kcal/mol)
-2997.98087630 -2997.97985772 -2997.97817345 -2997.97423567
-1881259.9817 -1881259.3425 -1881258.2856 -1881255.8147
Energy differences (Hartree) (kcal/mol) 0.00000 -0.00102 -0.00270 -0.00664
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Trans-cis (tc) Cis-trans (ct) Trans-trans (tt) Cis-cis (cc)
(Hartree)
0.00 -0.64 -1.69 -4.17
Dipole Moment (Debye) 2.6601 4.1032 5.8541 1.9549
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Energy Conformers
ACCEPTED MANUSCRIPT Table 2. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ23 υ24 υ25 υ26 υ27
Raman
3340 3097 3061 3046 1586 1555 1463 1380 1344 1296 1234 1177 1134 1088 1057 1030 937
3097 3062 3047 1581 1551 1461 1380 1346 1295 1234 1175 1090 -
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υ19 υ20 υ21 υ22
υ13-12(100) υ8-2(91) υ7-3(91) υ9-5(100) υ3-2(27) + υ4-3(12) + υ15-14(11) + υ5-4(11) υ2-1(26) + υ4-3(24) + υ5-4(18) + υ6-1(10) υ15-4 (25) + υ3-2(20) υ15-12(26) + υ15-14(25) υ15-12(13) + υ15-4(11) + δ3-2-8(11) + δ7-3-2(11) υ15-14(19) + υ6-5(16) + υ15-12(12) + υ4-3(10) υ6-1(27) + υ6-5(24) + υ5-4(15) + υ2-1(14) δ6-5-9(21) + δ9-5-4(20) + δ8-2-1(14) + δ3-2-8(12) δ7-3-2(25) + υ3-2(22) + δ4-3-7(20) υ4-3(15) + δ9-5-4(15) + δ6-5-9(13) δ6-5-9(13) + υ6-1(10) υ6-1(18) + δ13-12-15(11) + δ8-2-1(10) δ15-14-11(67) + υ15-12(20) τ4-3-2-8(23) + τ8-2-1-10(20) + τ15-4-3-7(13) + τ7-3-2-1(13) + τ8-2-1-6(12) δ2-1-6(14) + υ15-4(11) τ5-6-1-2(14) + τ3-2-1-6(14) + τ1-6-5-4(10) τ14-15-12-13(25) + τ14-15-4-5(13) + τ12-15-4-3(12) δ1-6-5(20) + δ6-5-4(15) + δ4-3-2(14) + δ3-2-1(14) δ12-15-14(16) + υ15-4(15) + υ10-1(12) + δ5-4-3(10) τ12-15-14-11(24) + τ4-15-12-13(14) τ4-15-14-11(32) + τ12-15-14-11(22) δ4-15-12(27) + δ4-15-14(22) + δ5-4-15(14) + δ15-4-3(13) δ12-15-14(34) + υ10-1(29) + δ4-5-14(11)
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υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9 υ10 υ11 υ12 υ13 υ14 υ15 υ16 υ17 υ18
IR
B3LYP / 6-311++G(d,p) Unscaled SQM IIR Freq. 3887 3340 22.32 3212 3105 0.16 3186 3079 0.23 3124 3019 9.11 1614 1592 51.25 1580 1553 12.53 1494 1464 7.97 1411 1376 48.97 1369 1349 100.00 1357 1303 37.59 1326 1236 5.47 1276 1171 4.10 1158 1130 1.60 1138 1089 34.62 1092 1061 20.50 1019 1013 41.23 979 942 27.79
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Assignments
SC
Mode
EP
21.06 14.04 21.38 52.81 3.37 2.56 0.84 23.82 4.74 3.89 1.62 1.10 -
841 803 740 665
774 650
853 778 758 672
838 779 738 658
3.19 8.20 4.10 15.49
29.16 0.09
611
591 -
642
631
0.68
10.44
549 474 458
474 441
567 472 451
571 461 442
5.47 22.55 15.72
1.56 1.08
422 404
429 404
431 401
430 398
0.91 1.37
2.78 0.58
IR: Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ, δ, τ: stretching, bending and torsion, respectively.
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ACCEPTED MANUSCRIPT Table 3. Experimental and calculated wavelengths (λ), excitation energies, of 6B3PBA in ethanol, methanol and water.
5.0906 In Methanol 243 5.0941 254 4.8850
H→L (64%), H→L+1 (24%), H-3→L (6%), H-3→L+1 (4%) H→L (64%), H-2→L+1 (2%)
224
5.5350
267
4.6436
π→π* π→π*
H-1→L+1 (97%), H-2→L+1 (2%) H→L (64%), H→L+1 (24%), H-3→L (6%), H-3→L+1 (4%)
223 267
5.5598 4.6436
π→π* π→π*
H→L+2 (94%), H→L+3 (4%) H→L (64%), H→L+1 (24%), H-3→L (6%), H-3→L+1 (4%)
219 267
5.6614 4.6436
π→π*
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In Water 219 5.6599 254 4.8857
λ (nm) E (eV) Experimental
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254
Major contributes
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λ (nm) E (eV) Assignments B3LYP/6-311++G(d, p) In Ethanol 244 4.8119 π→π*
ACCEPTED MANUSCRIPT Figures Figure 1. Possible conformers of 6B3PBA. Figure 2. 13C NMR spectrum of 6B3PBA.
Figure 4. COSY NMR spectrum of 6B3PBA. Figure 5. 1H coupled 13C NMR spectrum of 6B3PBA. Figure 6. HETCOR NMR spectrum of 6B3PBA.
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Figure 3. 1H NMR spectrum of 6B3PBA.
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Figure 7. Experimental (A) and scaled calculated (B) Infrared spectrum of 6B3PBA. Figure 8. Experimental (A) and scaled calculated (B) Raman spectrum of 6B3PBA.
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Figure 9. Experimental and theoretical UV-VIS spectra of 6B3PBA in water, ethanol and
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methanol.
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cis-cis (cc)
trans-trans (tt)
SC
Trans-cis (tc)
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Figure 1. Possible conformers of 6B3PB
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Figure 1. Possible conformers of 6B3PBA.
cis-trans (ct)
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Figure 2. 13C NMR spectrum of 6B3PBA.
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Figure 3. 1H NMR spectrum of 6B3PBA.
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Figure 4. COSY NMR spectrum of 6B3PBA.
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Figure 5. 1H coupled 13C NMR spectrum of 6B3PBA.
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Figure 6. HETCOR NMR spectrum of 6B3PBA.
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Figure 7. Experimental (A) and scaled calculated (B) Infrared spectrum of 6B3PBA.
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Figure 8. Experimental (A) and scaled calculated (B) Raman spectrum of 6B3PBA.
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Figure 9. Experimental and theoretical UV-VIS spectra of 6B3PBA in water, ethanol and methanol.
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NMR study
UV-Vis study
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DFT study of 6-Bromo-3-Pyridinyl Boronic Acid
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FT-IR and Raman studies
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Supplementary Figures Figure S1. Theoretical IR and Raman spectra in different bases sets. Figure S2. Plot of the experimental and theoretical vibrational frequencies of 6B3PBA
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molecule. Figure S3. Atomic orbital compositions of the frontier molecular orbital for 6B3PBA.
Figure S4. The molecular electrostatic potential 3D map and 2D counter map for 6B3PBA
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molecule.
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Figure S1. Theoretical IR and Raman spectra in different base sets.
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Figure S2. Plot of the experimental and theoretical vibrational frequencies of 6B3PBA molecule.
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Figure S2. (continued)
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Figure S3. Atomic orbital compositions of the frontier molecular orbital for 6B3PBA.
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Figure S4. The molecular electrostatic potential 3D map (A) and 2D counter map (B) for 6B3PBA molecule.
ACCEPTED MANUSCRIPT Supplementary Tables Table S1. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-311G(d, p) method) of 6B3PBA in gas phase.
(B3LYP/6-311G(d) method) of 6B3PBA in gas phase.
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Table S2. Comparison of the experimental and calculated vibrational wavenumbers (cm-1)
(B3LYP/6-31G(d, p) method) of 6B3PBA in gas phase.
SC
Table S3. Comparison of the experimental and calculated vibrational wavenumbers (cm-1)
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Table S4. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-31G(d) method) of 6B3PBA in gas phase.
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Table S5. The calculated energy values and the energy gaps of 6B3PBA molecule.
ACCEPTED MANUSCRIPT Table S1. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-311G(d,p) method) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ23 υ24 υ25 υ26 υ27
IR
Raman
3340 3097 3061 3046 1586 1555 1463 1380 1344 1296 1234 1177 1134 1088 1057 1030 937
3097 3062 3047 1581 1551 1461 1380 1346 1295 1234 1175 1090 -
841 803 740 665
774 650
840 761 747 657
845 772 739 657
3.37 9.46 4.49 17.09
25.45 0.51
611
591
627
626
0.76
9.53
549 474
474
555 465
566 465
5.57 25.81
1.20
458
441
445
444
11.48
2.32
422 404
429 404
422 393
424 396
0.79 1.10
2.38 1.01
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υ19 υ20 υ21 υ22
υ13-12(100) υ8-2(91) υ7-3(91) υ9-5(100) υ3-2(28) + υ5-4(13) + υ4-3(11) + υ15-4(10) υ4-3(27) + υ2-1(26) + υ5-4(16) υ15-4 (22) + υ3-2(22) + υ5-4(10) υ15-14(26) + υ15-12(15) + υ2-1(10) υ15-12(25) + υ15-4(11) υ15-14(22) + υ4-3(12) + υ6-5(10) + υ15-12(10) υ2-1(21) + δ6-5-9(20) + υ6-1(14) + δ9-5-4(10) υ6-5(27) + δ6-5-9(17) + δ9-5-4(14) + υ6-1(13) υ3-2(28) + δ7-3-2(20) + δ4-3-7(15) υ4-3(15) + δ13-12-15 (14) + δ6-5-9(10) υ6-5(10) + υ10-1(10) υ6-1(18) + δ13-12-15(11) + δ8-2-1(10) δ15-14-11(42) + υ15-12(26) + υ15-14(11) τ4-3-2-8(23) + τ8-2-1-10(21) + τ15-4-3-7(13) + τ8-2-1-6(13) + τ7-3-2-1(12) δ2-1-6(14) + υ15-4(11) τ5-6-1-2(15) + τ3-2-1-6(14) + τ1-6-5-4(10) τ14-15-12-13(30)+τ14-15-4-5(12)+τ12-15-4-3(12) δ1-6-5(21) + δ6-5-4(15) + δ4-3-2(14) + δ3-2-1(14) δ12-15-14(16) + υ15-4(15) + υ10-1(13) + δ5-4-3(10) τ12-15-14-11(34) + τ4-15-12-13(13) τ4-15-14-11(26) + τ12-15-14-11(14) + τ5-4-3-2(10) δ4-15-12(27) + δ4-15-14(22) + δ5-4-15(14) + δ15-4-3(13) δ12-15-14(34) + υ10-1(29) + δ4-15-14(11)
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υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9 υ10 υ11 υ12 υ13 υ14 υ15 υ16 υ17 υ18
B3LYP / 6-311G(d,p) Scaled SQM IIR Freq. 3672 3340 20.88 3068 3106 0.31 3044 3081 0.32 2980 3016 10.52 1579 1593 50.25 1548 1557 13.22 1461 1460 9.11 1394 1372 49.48 1344 1351 100 1330 1297 29.49 1298 1221 4.26 1249 1181 3.26 1131 1135 1.45 1115 1103 31.12 1068 1051 24.38 1003 1008 37.17 967 951 30.30
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Assignments
SC
Mode
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EP
Scaled with 0.955 above 1800cm−1, 0.977 under 1800cm−1. IR:Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ,δ,τ: stretching, bending and torsion, respectively.
IR 19.95 13.68 22.02 47.83 2.64 1.77 0.83 20.16 4.11 2.83 1.76 0.72 -
ACCEPTED MANUSCRIPT Table S2. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-311G(d) method) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ23 υ24 υ25 υ26 υ27
Raman
3340 3097 3061 3046 1586 1555 1463 1380 1344 1296 1234
3097 3062 3047 1581 1551 1461 1380 1346 1295 1234
1177 1134 1088 1057 1030 937
1175 1090 -
841 803 740 665
B3LYP / 6-311G(d) SQM IIR 14.05 0.78 0.49 12.67 50.72 13.36 10.07 50.47 100 35.03 4.79
20.09 12.96 21.42 47.61 2.44 1.32 0.88 19.66 4.26 3.24
1250 1136 1118 1069 1007 967
1173 1136 1104 1049 1009 949
3.43 1.34 33.75 24.86 33.22 32.60
1.61 0.64 -
774 650
836 761 747 664
838 770 735 661
3.65 9.82 4.90 22.37
25.50 0.48
611
591
628
629
0.80
9.58
549
-
553
564
6.31
-
474 458
474 441
473 451
472 447
38.36 5.20
1.48 1.90
422 404
429 404
421 396
424 394
0.98 0.75
2.52 0.94
Scaled with 0.955 above 1800cm−1, 0.977 under 1800cm−1. IR:Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ,δ,τ: stretching, bending and torsion, respectively.
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IR
3340 3105 3082 3015 1594 1556 1459 1374 1353 1297 1229
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υ19 υ20 υ21 υ22
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υ13 υ14 υ15 υ16 υ17 υ18
υ13-12(100) υ8-2(89) + υ7-3(11) υ7-3(89) + υ8-2(11) υ9-5(100) υ3-2(27) + υ5-4(13) + υ4-3(10) + υ15-4(10) υ2-1(26) + υ4-3(27) + υ5-4(15) υ15-4 (21) + υ3-2(23) + υ5-4(11) υ15-12(11) + υ15-14(26) υ15-12(31) + υ15-4(10) υ15-14(21) + υ4-3(13) + δ9-5-4(13) υ2-1(23) + δ8-2-1(12) + δ9-5-4(16) + δ6-5-9(21) δ7-3-2(11) + δ4-3-7(12) + υ5-4(15) + υ6-1(14) + υ6-5(23) δ7-3-2(12) + υ3-2(33) + δ3-2-8(10) υ4-3(14) + υ6-5(17) + δ13-12-15 (13) δ 6-5-4(10) + υ6-5(10) δ13-12-15(59) + δ15-14-11(10) + υ15-14(16) δ15-14-11(37) + υ15-12(25) + υ15-14(12) τ4-3-2-8(23) + τ8-2-1-10(20) + τ15-4-3-7(13) + τ7-3-2-1(12) + τ8-2-1-6(13) δ2-1-6(14) + υ15-4(11) τ5-6-1-2(15) + τ3-2-1-6(14) + τ1-6-5-4(10) τ14-15-12-13(36)+τ14-15-4-5(11)+τ12-15-4-3(11) δ1-6-5(21) + δ6-5-4(15) + δ4-3-2(14) + δ3-2-1(14) δ12-15-14(16) + υ15-4(16) + υ10-1(13) + δ5-4-3(10) τ12-15-14-11(20) + τ4-15-12-13(11) + τ12-15-14-11(45) τ4-15-14-11(17) + τ5-4-3-2(11) δ4-15-12(27) + δ4-15-14(22) + δ5-4-15(15) + δ15-4-3(13) δ12-15-14(34) + υ10-1(28) + δ4-15-14(12)
EP
υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9 υ10 υ11 υ12
IR
Scaled Freq. 3638 3071 3048 2982 1584 1551 1468 1396 1348 1335 1304
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Assignments
SC
Mode
ACCEPTED MANUSCRIPT Table S3. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-31G(d,p) method) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ15 υ16 υ17 υ18 υ19 υ20 υ21 υ22 υ23 υ24 υ25 υ26 υ27
Raman
3340 3097 3061 3046 1586 1555 1463 1380
3097 3062 3047 1581 1551 1461 1380
1344 1296 1234
1346 1295 1234
1177 1134
1175 -
B3LYP / 6-31G(d,p) SQM IIR 20.24 0.38 0.48 14.06 57.93 15.18 9.19 60.02
18.22 13.35 20.56 49.99 1.77 1.41 1.14
1357 1341 1307
1350 1299 1240
100 53.90 3.80
18.47 7.06 2.82
1271 1136
1172 1131
3.13 2.07
-
1.49
1088 1057 1030 937
1090 -
1120 1076 1001 969
1092 1056 1011 943
36.33 25.14 45.58 37.77
1.56 -
841 803 740 665
774 650
843 760 748 644
846 771 744 645
3.54 11.14 3.21 19.30
23.94 0.35
611
591
626
629
1.02
9.63
549 474 458
474 441
556 467 448
567 467 448
6.33 26.74 19.33
2.47 3.12
422
429
423
430
0.84
2.42
404
404
396
399
2.04
0.81
Scaled with 0.955 above 1800cm−1, 0.977 under 1800cm−1. IR:Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ,δ,τ: stretching, bending and torsion, respectively.
AC C
IR
3340 3108 3082 3012 1593 1553 1461 1376
M AN U
υ13 υ14
TE D
υ10 υ11 υ12
υ13-12(100) υ8-2(92) υ7-3(93) υ9-5(100) υ3-2(28) + υ4-3(13) + υ15-4(10) + υ5-4(11) υ2-1(27) + υ4-3(24) + υ5-4(17) υ15-4 (23) + υ3-2(20) υ15-12(22) + υ15-14(23) + υ2-1(10) υ15-12(15) + υ15-4(12) + δ3-2-8(10) + δ7-3-2(10) υ15-14(21) + υ6-5(15) + υ15-12(13) + υ4-3(10) υ6-1(26) + υ6-5(23) + υ5-4(15) + υ2-1(15) δ6-5-9(21) + δ9-5-4(20) + υ6-5(10) + δ8-2-1(14) + δ3-2-8(12) δ7-3-2(25) + υ3-2(23) + δ4-3-7(19) υ4-3(14) + δ9-5-4(14) + δ6-5-9(14) + δ13-12-15 (12) υ6-5(10) + υ6-1(11) + δ6-5-9(11) υ6-1(17) + δ13-12-15(19) δ15-14-11(48) + υ15-12(25) + υ15-14(10) τ4-3-2-8(23) + τ8-2-1-10(22) + τ15-4-3-7(12) + τ7-3-2-1(13) + τ8-2-1-6(12) δ2-1-6(14) + υ15-4(10) τ5-6-1-2(16) + τ3-2-1-6(15) + τ1-6-5-4(11) τ14-15-12-13(30)+τ14-15-4-5(14)+τ12-15-4-3(13) δ1-6-5(20) + δ6-5-4(15) + δ4-3-2(14) + δ3-21(14) δ12-15-14(17) + υ15-4(14) + υ10-1(12) + δ5-4-3(10) τ12-15-14-11(26) + τ4-15-12-13(15) τ4-15-14-11(32) + τ12-15-14-11(21) δ4-15-12(26) + δ4-15-14(23) + δ5-4-15(14) + δ15-4-3(12) δ12-15-14(33) + υ10-1(29) + δ4-15-14(10) + υ15-4(10)
EP
υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9
IR
Scaled Freq. 3437 3087 3061 2990 1595 1560 1473 1414
RI PT
Assignments
SC
Mode
ACCEPTED MANUSCRIPT Table S4. Comparison of the experimental and calculated vibrational wavenumbers (cm-1) (B3LYP/6-31G(d) method) of 6B3PBA in gas phase. Experimental
TED (≥ 10 %)
υ19 υ20 υ21 υ22 υ23 υ24 υ25 υ26 υ27
Raman
3340 3097 3061 3046 1586 1555 1463 1380 1344 1296 1234
3097 3062 3047 1581 1551 1461 1380 1346 1295 1234
1177 1134
1175 -
1088 1057 1030 937
B3LYP / 6-31G(d) SQM IIR 19.67 0.53 0.58 15.53 59.56 15.41 10.60 61.86 100 61.36 4.17
18.18 13.01 20.27 50.31 1.71 21.38 1.07 18.22 7.49 3.06
1272 1142
1176 1139
3.33 1.77
1.36 -
1090 -
1124 1077 1006 974
1100 1048 1010 947
39.44 26.97 39.47 36.96
1.18 -
841 803 740 665
774 650
843 760 748 645
844 767 743 645
3.93 11.55 3.34 20.94
21.28 0.58
611
591
627
626
1.05
9.61
549
-
555
564
6.62
-
474 458
474 441
471 452
470 451
36.96 13.43
2.35 2.75
422 404
429 404
423 398
426 397
0.90 1.39
2.46 0.87
Scaled with 0.955 above 1800cm−1, 0.977 under 1800cm−1. IR:Infrared; IIR and IR: Infrared and Raman intensities; Exp.: experimental. υ,δ,τ: stretching, bending and torsion, respectively.
AC C
IR
3340 3107 3082 3013 1595 1557 1460 1375 1352 1297 1227
M AN U
υ15 υ16 υ17 υ18
TE D
υ13 υ14
υ13-12(100) υ8-2(91) υ7-3(91) υ9-5(100) υ3-2(27) + υ4-3(13) + υ15-4(10) + υ5-4(11) υ2-1(28) + υ4-3(24) + υ5-4(16) υ15-4 (22) + υ3-2(21) + υ5-4(11) υ15-12(10) + υ15-14(23) + υ2-1(10) υ15-12(26) + υ15-4(10) υ15-14(24) + υ6-5(10) + υ15-12(13) + υ4-3(11) υ6-1(19) + υ6-5(17) + υ5-4(13) + υ2-1(19) δ6-5-9(17) + δ9-5-4(18) + υ6-5(10) + δ8-2-1(14) + δ3-2-8(14) + υ6-5(16) δ7-3-2(21) + υ3-2(24) + δ4-3-7(15) υ4-3(15) + δ9-5-4(14) + δ6-5-9(14) + δ13-12-15 (12) + δ15-14-11(11) υ6-5(10) υ6-1(12) + δ13-12-15(45) δ15-14-11(35) + υ15-12(26) + υ15-14(14) τ4-3-2-8(23) + τ8-2-1-10(21) + τ15-4-3-7(13) + τ7-3-2-1(13) + τ8-2-1-6(12) δ2-1-6(14) + υ15-4(10) τ5-6-1-2(16) + τ3-2-1-6(15) + τ1-6-5-4(11) τ14-15-12-13(32)+τ14-15-4-5(13)+τ12-15-4-3(13) δ1-6-5(21) + δ6-5-4(15) + δ4-3-2(14) + δ3-2-1(14) δ12-15-14(16) + υ15-4(15) + υ10-1(12) + δ5-4-3(10) τ12-15-14-11(36) + τ4-15-12-13(14) + τ4-15-14-11(12) τ4-15-14-11(26) + τ12-15-14-11(13) δ4-15-12(23) + δ4-15-14(26) + δ5-4-15(14) + δ15-4-3(13) δ12-15-14(33) + υ10-1(29) + δ4-15-14(10)
EP
υ1 υ2 υ3 υ4 υ5 υ6 υ7 υ8 υ9 υ10 υ11 υ12
IR
Scaled Freq. 3599 3092 3068 2999 1598 1562 1479 1413 1358 1346 1313
RI PT
Assignments
SC
Mode
ACCEPTED MANUSCRIPT
AC C
EP
TE D
M AN U
EHOMO (eV) ELUMO (eV) EHOMO-1 (eV) ELUMO+1 (eV) ELUMO+2 (eV) EHOMO-LUMO (eV) EHOMO-1-LUMO (eV) EHOMO-LUMO+1 (eV) EHOMO-1-LUMO+1 (eV) EHOMO-LUMO+2 (eV) EHOMO-1-LUMO+2 (eV)
SC
Monomer (in gas phase) -7.33 -1.77 -7.79 -1.47 0.75 5.56 6.02 5.86 6.32 6.58 7.04
B3LYP/ 6-311++G(d,p)
RI PT
Table S5. The calculated energy values and the energy gaps of 6B3PBA molecule.