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Journal ArticleDOI

Synthesis, Vibrational Spectra, and DFT Simulations of 3-bromo-2-methyl-5-(4-nitrophenyl)thiophene

01 Nov 2017-Journal of Applied Spectroscopy (Springer)-Vol. 84, Iss: 5, pp 888-899

AbstractA new thiophene derivative, 3-bromo-2-methyl-5-(4-nitrophenyl)thiophene (2), was synthesized through the Suzuki coupling reaction of 4-bromo-5-methylthiophen-2-ylboronic acid (1) and 4-iodonitrobenzene, and its structure was confirmed by nuclear magnetic resonance (NMR), low and high resolution mass spectrometry (HRMS), Fourier transform infrared spectroscopy (FT-IR), and X-ray investigations of the crystal structure. The FT-IR spectra (4000–400 cm–1), Raman spectra (4000–100 cm–1), and theoretical vibrational frequencies of this new substance were investigated. Its theoretically established geometric parameters and calculated vibrational frequencies are in good agreement with the reported experimental data. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and other related parameters of the compound were calculated. The ionization potentials given by the B3LYP and HF (Hartree–Fock) methods for this new compound are –0.30456 and –0.30501 eV, respectively.

Topics: HOMO/LUMO (59%), Thiophene (56%), Raman spectroscopy (50%)

Summary (1 min read)

Synthesis of 3-bromo-2-methyl-5-(4-nitrophenyl)thiophene (2) (Scheme 1)

  • The mixture was left to cool to room temperature, after which it was extracted with diethyl ether (3-50 mL).
  • The obtained crude product was Computational Details.
  • The molecular properties, such as optimized geometric parameters and vibrational wave numbers, were calculated using Gauss View molecular visualization [18] and Gaussian 09W [20] sofware.

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Citation for final published version:
Balakit, A. A., Sert, Y., Çırak, Ç., Smith, Keith, Kariuki, Benson and El-Hiti, G. A. 2017. Synthesis,
vibrational spectra, and DFT simulations of 3-bromo-2-methyl-5-(4-nitrophenyl)thiophene. Journal
of Applied Spectroscopy 84 (5) , pp. 888-899. 10.1007/s10812-017-0561-9 file
Publishers page: http://dx.doi.org/10.1007/s10812-017-0561-9 <http://dx.doi.org/10.1007/s10812-
017-0561-9>
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made available in ORCA are retained by the copyright holders.

SYNTHESIS, VIBRATIONAL SPECTRA, AND DFT SIMULATIONS
OF 3-BROMO-2-METHYL-5-(4-NITROPHENYL)THIOPHENE
A. A. Balakit,
a*
Y. Sert,
b,c*
Ç. Çırak,
d
K. Smith,
e
UDC 535.375.5;543.42
B. M. Kariuki,
e
and G. A. El-Hiti
f*
A new thiophene derivative, 3-bromo-2-methyl-5-(4-nitrophenyl)thiophene (2), was synthesized through the Suzuki
coupling reaction of 4-bromo-5-methylthiophen-2-ylboronic acid (1) and 4-iodonitrobenzene, and its structure was
confirmed by nuclear magnetic resonance (NMR), low and high resolution mass spectrometry (HRMS), Fourier
transform infrared spectroscopy (FT-IR), and X-ray investigations of the crystal structure. The FT-IR spectra
(4000400 cm
1
), Raman spectra (4000100 cm
1
), and theoretical vibrational frequencies of this new substance
were investigated. Its theoretically established geometric parameters and calculated vibrational frequencies are in
good agreement with the reported experimental data. The highest occupied molecular orbital (HOMO) and lowest
unoccupied molecular orbital (LUMO) energies and other related parameters of the compound were calculated.
The ionization potentials given by the B3LYP and HF (HartreeFock) methods for this new compound are
0.30456 and 0.30501 eV, respectively.
Keywords: FT-IR spectra, Raman spectra, 3-bromo-2-methyl-5-(4-nitrophenyl)thiophene, vibrational frequencies,
frontier molecular orbital.
Introduction. Thiophene derivatives are important compounds that can be used as precursors for the synthesis of
materials. They are of great interest due to numerous applications in photoswitching [1, 2], nanotechnologies [3, 4], and
biosensorics [5]. Aryl thiophenes are usually synthesized via metal catalyzed cross-coupling processes, such as the Suzuki,
Negishi, and Stille reactions, in which the organometallic derivatives of thiophene undergo coupling reactions with aryl
halides [6, 7]. Also, aryl thiophenes can be synthesized by palladium-catalyzed direct arylation of substituted thiophenes
with aryl bromides [8]. 3-Bromo-2-methyl-5-phenylthiophene is one of the most frequently used derivatives. It is usually
synthesized via the Suzuki coupling reaction [9, 10].
For our studies of the synthesis and optical properties of various heterocycles [1116], we synthesized 3-bromo-2-
methyl-5-(4-nitrophenyl)thiophene (2) and for the first time established its molecular and crystal structures using the
methods of Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, and quantum chemical calculations for
determining the vibrational frequencies.
Experimental. Characterization techniques. A Gallenkamp melting point apparatus was used to determine the melting
point.
1
H (400 MHz) and
13
C NMR (100 MHz) spectra were recorded in CDCl
3
on a Bruker AV400 spectrometer. Chemical
shifts δ (ppm) are reported relative to TMS, and coupling constants (J) are in Hz. A Waters GCT Premier Spectrometer was used
to record the mass spectrum. A Waters LCT Premier XE setup was used to record the accurate mass of the molecular ion peak. A
Perkin-Elmer Spectrum Two FT-IR Spectrometer was used to record the IR spectrum (4000400 cm
1
). A Renishaw Invia
Raman spectrophotometer was used to record the Raman spectrum (4000100 cm
1
). X-ray crystallographic data were collected
at 150 K on a Nonius Kappa CCD diffractometer using graphite monochromated MoK
α
radiation
_____________________
*
To whom correspondence should be addressed.
a
College of Pharmacy, University of Babylon, P.O. Box 4, Babylon, Iraq; email: asim_alsalehi@hotmail.com;
b
Bozok University, Department of Physics, Faculty of Art & Sciences, Yozgat 66100, Turkey;
c
Sorgun Vocational School,
Bozok University, Yozgat 66100, Turkey; email: yusufsert1984@gmail.com;
d
Erzincan University, Department of
Physics, Faculty of Art & Sciences, Erzincan 24100, Turkey;
e
School of Chemistry, Cardiff University, Main Building,
Park Place, Cardiff CF10 3AT, UK;
f
Cornea Research Chair, Department of Optometry, College of Applied Medical
Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Saudi Arabia; email: gelhiti@ksu.edu.sa. Abstract of
article is published in Zhur-nal Prikladnoi Spektroskopii, Vol. 84, No. 5, p. 834, SeptemberOctober, 2017.
888

(
MoK
α
= 0.71073 Å) equipped with an Oxford Cryosystem of cooling. The structures were solved using direct methods
and refined with SHELX [17]. It is established that the structure is a two-component inversion twin. There are two
molecules in the asymmetric unit, and the thiophene group is disordered in both with occupancies of 0.129(4)/0.871(4) and
0.342(4)/0.658(4). The molecule geometry was reconstructed with the help of the data provided by The Cambridge
Crystallographic Data Centre (www.ccdc.cam.ac.uk/structures).
Synthesis of 3-bromo-2-methyl-5-(4-nitrophenyl)thiophene (2) (Scheme 1). A mixture of 3-bromo-2-methylthiophen-5-
ylboronic acid (1) (1.00 g, 4.53 mmol), 4-iodonitrobenzene (1.00 g, 4.02 mmol), anhydrous sodium carbonate (1.28 g, 12.10
mmol), and tetrakis(triphenylphosphine)palladium(0) (0.12 g, 0.11 mmol) in tetrahydrofuran (30 mL, containing 10% water) was
refluxed at 90
ο
C for 16 h. The mixture was left to cool to room temperature, after which it was extracted with diethyl ether (350
mL). The organic layer was separated, dried (MgSO
4
), and evaporated under reduced pressure. The obtained crude product was
purified by column chromatography (silica gel; petroleum ether 4060
ο
C/ethyl acetate 97:3 by volume) to give compound 2
(1.00 g, 3.35 mmol; 83%). Crystallization from diethyl ether gave yellow crystals m.p. 131132
ο
C.
1
H NMR, δ: 8.15 (d, J = 8.8,
2H, H-3/H-5 of Ar), 7.56 (d, J = 8.8, 2H, H-2/H-6 of Ar), 7.2 (s, 1H, H-4), and 2.38 (s, 3H, CH
3
).
13
C NMR, δ: 146.7 (s, C-4 of
Ar), 139.5 (s, C-1 of Ar), 138.2 (s, C-5), 137.0 (s, C-2), 128.2 (d, C-4),
125.4 (d, C-2/C-6 of Ar), 124.5 (d, C-3/C-5 of Ar), 111.0 (s, C-3) and 15.1 (q, CH
3
). EI-MS (m/z, %): 299 ([M
81
Br]
+
, 92),
297 ([M
79
Br]
+
, 94), 269 (100), 267 (93), 188 (20), 171 (70). HRMS (EI): Found, 296.9452. Calculated for C
11
H
8
NO
2
SBr
[M
79
Br]
+
296.9459.
Scheme 1. Synthesis of 3-bromo-2-methyl-5-(4-nitrophenyl)thiophene (2).
Computational Details. Initial atomic coordinates were determined using the Gauss View software database and
experimental XRD data to optimize the input structure to obtain the most stable structure [18]. The DFT/B3LYP and HF
methods with the 6-311++G(d,p) basis set were used to calculate the molecular structures (gas phase ground state) of
compound 2. The vibrational frequencies were then found for the calculated optimized structure. The calculated harmonic
vibrational frequencies were scaled by 0.9614 (B3LYP) and 0.9051 (HF) for the use with the 6-311++G(d,p) basis set,
respectively [18, 19]. The molecular properties, such as optimized geometric parameters and vibrational wave numbers,
were calculated using Gauss View molecular visualization [18] and Gaussian 09W [20] sofware. The calculated vibrational
frequencies were assigned via potential energy distribution (PED) analysis of all the fundamental vibration modes by using
VEDA 4 software [21, 22]. All the vibrational assignments were based on the B3LYP/6-311++G(d,p) level calculations.
Therefore, some assignments might correspond to the value of the previous or next vibrational frequency at the HF/6-
311++G(d,p) level.
Results and Discussion. Geometric structure. The X-ray analysis of the crystal structure of compound (C
11
H
8
BrNO
2
S)
(2) showed an orthorhombic system with the Pca2
1
space group. It showed the following cell dimensions: a = 26.1513 Å, b =
3.8859 Å, c = 21.3942 Å, α = 90
o
, = 90
o
, = 90
o
, and V = 2174.11 Å
3
. Since there are two molecules in the asymmetric unit
and the thiophene group is disordered in both, the crystal contains four distinct sets of bond lengths and angles, although they are
all very similar. Consequently, just one representative set was used in order to compare the experimental and compu-tational
values. The bond lengths and bond angles for the selected experimental (X-ray) and optimized theoretical structures are shown in
Table 1. The structure of 2 with the atom numbering scheme used for Table 1 is represented in Fig. 1.
The bond length of the C1C4 bond, at 1.361(11) Å, is similar to the bonds in other thiophene derivatives, which
are typically around 1.361.38 Å [2325]. The C2C3 and C3Br11 bonds, at 1.283(7) and 1.824(8)Å, respectively, are
significantly shorter than similar bonds in other thiophene derivatives (typically 1.351.37 Å [2325] and 1.861.90 [26
28]).These differences may be due to the nature of the packing in the crystal structure. Both calculation methods also
underestimated the length of the C3C4 bond and consistently overestimated the lengths of the C-H bonds. However, the
C2C7 bond length, experimentally observed as 1.470(9) Å, was similar to the calculated value (1.496 (B3LYP) or 1.501
(HF)) and to the experimental values for similar bonds in related compounds (1.505 [29] and 1.490 Å [30]). So, there was
good agreement between the experimental and calculated values of the bonds. The linear regression correlation coefficients
(R
2
) were reasonable (0.951 for B3LYP and 0.945 for HF).
889

Fig. 1. The numbering of atoms of the molecule of 2.
(a) (b)
Fig 2. Comparison of observed and calculated infrared (a) and Raman (b) spectra of 2.
The linear regression correlation coefficients (R
2
) were less (0.848 for B3LYP and 0.876 for HF) for the calculated
bond angles in compound 2. Many of the calculated bond angles showed a reasonable correlation with the observed angles,
but the largest variations ((9.6/9.0 for B3LYP/HF (S5C2C7), 7.5/7.1 (C3C2S5), 6.7/5.3 (C2C3Br11), 5.4/5.1 (C1
C4C3), 5.7/4.8 (C4C3Br11) and 3.1/3.2
o
(C3C4H6)) were for the angles of the bonds inside the thiophene ring and
around it, which resulted in decreasing the linear regression coefficients.
890

TABLE 1. Experimental and Calculated Geometric Parameters for Сompound 2
Geometric parameters
Experimental
B3LYP/6-311++G(d,p)
HF/6-311++G(d,p)
Bond lengths, Å
C1C4
1.361(11)
1.373
1.347
C1S5
1.735(8)
1.753
1.738
C1C12
1.466(13)
1.463
1.477
C2C3
1.283(7)
1.369
1.344
C2S5
1.736(8)
1.742
1.734
C2C7
1.470(9)
1.496
1.501
C3C4
1.501(11)
1.420
1.433
C3Br11
1.824(8)
1.906
1.891
C4H6
0.950
1.081
1.072
C7H8
0.980
1.093
1.082
C7H9
0.980
1.091
1.084
C7H10
0.980
1.095
1.086
C12C13
1.404(14)
1.407
1.393
C12C14
1.390(14)
1.408
1.394
C13C15
1.390(15)
1.387
1.381
C13H16
0.950
1.084
1.074
C14C17
1.381(15)
1.386
1.380
Bond lengths, Å
C14H18
0.950
1.083
1.074
C15C19
1.371(16)
1.391
1.381
C15H20
0.950
1.081
1.072
C17C19
1.376(16)
1.392
1.382
C17H21
0.950
1.081
1.072
C19N22
1.491(13)
1.473
1.464
N22O23
1.235(13)
1.226
1.188
N22O24
1.209(12)
1.226
1.188
R
2
0.9507
0.9454
Bond angles, degrees
C4C1S5
111.1(8)
110.0
110.5
C4C1C12
130.6(9)
128.4
127.6
S5C1C12
118.3(6)
121.7
121.8
C3C2S5
117.0(6)
109.1
109.5
C3C2C7
135.1(10)
129.5
129.9
S5C2C7
107.8(9)
121.3
120.6
C2C3C4
108.9(8)
115.2
114.8
C2C3Br11
129.3(6)
122.8
124.2
891

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References
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TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
Abstract: An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.

77,177 citations


Journal ArticleDOI
Masahiro Irie1

3,444 citations


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Abstract: PREFACE. CONTRIBUTORS. INTRODUCTION AND BACKGROUND. Historical Background of Organopalladium Chemistry Fundamental Properties of Palladium and Patterns of the Reactions of Palladium and Its Complexes. PALLADIUM COMPOUNDS: STOICHIOMETRIC PREPARATION, IN SITU GENERATION, AND SOME PHYSICAL AND CHEMICAL PROPERTIES. Background for Part II. Pd(0) and Pd(II) Compounds Without Carbon-Palladium Bonds. Organopalladium Compounds Containing Pd(0) and Pd(II). Palladium Complexes Containing Pd(I), Pd(III), or Pd(IV). PALLADIUM-CATALYZED REACTIONS INVOLVING REDUCTIVE ELIMINATION. Background for Part III. Palladium-Catalyzed Carbon-Carbon Cross-Coupling. Palladium-Catalyzed Carbon-Hydrogen and Carbon- Heteroatom Coupling. PALLADIUM-CATALYZED REACTIONS INVOLVING CARBOPALLADATION. Background for Part IV. The Heck Reaction (Alkene Substitution via Carbopalladation- Dehydropalladation) and Related Carbopalladation Reactions. Palladium-Catalyzed Tandem and Cascade Carbopalladation of Alkynes and 1,1-Disubstituted Alkenes. Allylpalladation and Related Reactions of Alkenes, Alkynes, Dienes, and Other -Compounds. Alkynyl Substitution via Alkynylpalladation-Reductive Elimination. Arene Substitution via Addition-Elimination. Carbopalladation of Allenes. Synthesis of Natural Products via Carbopalladation. Cyclopropanation and Other Reactions of Palladium-Carbene (and Carbyne) Complexes. Carbopalladation via Palladacyclopropanes and Palladacyclopropenes. Palladium-Catalyzed Carbozincation. PALLADIUM-CATALYZED REACTIONS INVOLVING NUCLEOPHILIC ATTACK ON LIGANDS. Background for Part V. Palladium-Catalyzed Nucleophilic Substitution Involving Allylpalladium, Propargylpalladium, and Related Derivatives. Palladium-Catalyzed Reactions Involving Nucleophilic Attack on -Ligands of Palladium-Alkene, Palladium-Alkyne, and Related Derivatives. PALLADIUM-CATALYZED CARBONYLATION AND OTHER RELATED REACTIONS INVOLVING MIGRATORY INSERTION. Background for Part VI. Migratory Insertion Reactions of Alkyl-, Aryl-, Alkenyl-, and Alkynylpalladium Derivatives Involving Carbon Monoxide and Related Derivatives. Migratory Insertion Reactions of Allyl, Propargyl, and Allenylpalladium Derivatives Involving Carbon Monoxide and Related Derivatives. Acylpalladation and Related Addition Reactions. Other Reactions of Acylpalladium Derivatives. Synthesis of Natural Products via Palladium-Catalyzed Carbonylation. Palladium-Catalyzed Carbonylative Oxidation. Synthesis of Oligomeric and Polymeric Materials via Palladium-Catalyzed Successive Migratory Insertion of Isonitriles. CATALYTIC HYDROGENATION AND OTHER PALLADIUM-CATALYZED REACTIONS VIA HYDROPALLADATION, METALLOPALLADATION, AND OTHER RELATED SYN ADDITION REACTIONS WITHOUT CARBON-CARBON BOND FORMATION OR CLEAVAGE. Background for Part VII. Palladium-Catalyzed Hydrogenation. Palladium-Catalyzed Isomerization of Alkenes, Alkynes, and Related Compounds without Skeletal Rearrangements. Palladium-Catalyzed Hydrometallation. Metallopalladation. Palladium-Catalyzed Syn-Addition Reactions of X-Pd Bonds (X = Group 15, 16, and 17 Elements). PALLADIUM-CATALYZED OXIDATION REACTIONS THAT HAVE NOT BEEN DISCUSSED IN EARLIER PARTS. Background for Part VIII. Oxidation via Reductive Elimination of Pd(II) and Pd(IV) Complexes. Palladium-Catalyzed or -Promoted Oxidation via 1,2- or 1,4-Elimination. Other Miscellaneous Palladium-Catalyzed or -Promoted Oxidation Reactions. REARRANGEMENT AND OTHER MISCELLANEOUS REACTIONS CATALYZED BY PALLADIUM. Background for Part IX. Rearrangement Reactions Catalyzed by Palladium. TECHNOLOGICAL DEVELOPMENTS IN ORGANOPALLADIUM CHEMISTRY. Aqueous Palladium Catalysis. Palladium Catalysts Immobilized on Polymeric Supports. Organopalladium Reactions in Combinatorial Chemistry. REFERENCES. General Guidelines on References Pertaining to Palladium and Organopalladium Chemistry. Books (Monographs). Reviews and Accounts (as of September 1999). SUBJECT INDEX.

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"Synthesis, Vibrational Spectra, and..." refers background in this paper

  • ...In-plane aromatic C–H bending vibrations typically appear at 1300–1000 cm –1 [40]....

    [...]

  • ...C–H stretching vibrations generally resonate at 3100–3000 cm –1 , and this region is used for identification of such vibrations [40, 41]....

    [...]


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15 Jan 1994
Abstract: Normal Vibrations and Absorption Regions of CX3. Normal Vibrations and Absorption Regions of CH2X. Normal Vibrations and Absorption Regions of CHX2. Normal Vibrations and Absorption Regions of CHX. Normal Vibrations and Absorption Regions of CX2. Normal Vibrations and Absorption Regions of C(=X)Y. Normal Vibrations and Absorption Regions of Alkenes and Alkynes. Normal Vibrations and Absorption Regions of Nitrogen Compounds. Normal Vibrations and Absorption Regions of Oxy Compounds. Normal Vibrations and Absorption Regions of Sulfur Compounds. Normal Vibrations and Absorption Regions of Ring Structures. Index.

1,202 citations


"Synthesis, Vibrational Spectra, and..." refers background in this paper

  • ...The methyl twisting mode is often seen in the 1470–1440 cm –1 region [38]....

    [...]

  • ...CH3 stretching vibrations generally appear at 2950–3050 (asymmetric) and 2900−2950 cm –1 (symmetric) [38, 39]....

    [...]

  • ...For various methyl-containing thiophene derivatives, symmetric deformations (δsCH3) appear at 1380 ± 25 cm –1 [38]....

    [...]

  • ...Aromatic compounds carrying a methyl group display a methyl rocking mode (ρCH3) in the neighborhood of 1045 cm –1 [38], while a second rocking mode at 970 ± 70 cm –1 region [38] is difficult to find among the C–H out-of-plane deformations....

    [...]

  • ...CH3 symmetrical bending deformations (δsCH3) are typically at 1400–1485 cm –1 [38] and for compound 2 were calculated as 1437 (B3LYP)/1487 (HF) and 1420 (B3LYP)/1454 cm –1 (HF)....

    [...]