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Synthesis and theoretical studies on new amidodithiophosphonates
Accepted Manuscript Synthesis and Theoretical Studies on New Amidodithiophosphonates Cemal Aydemir, Mehmet Karakus, Prof. Dr., Izzet Kara, Aslı Öztürk Kiraz, Nuri Kolsuz PII:
S0022-2860(16)30057-6
DOI:
10.1016/j.molstruc.2016.01.057
Reference:
MOLSTR 22173
To appear in:
Journal of Molecular Structure
Received Date: 8 December 2015 Revised Date:
22 January 2016
Accepted Date: 22 January 2016
Please cite this article as: C. Aydemir, M. Karakus, I. Kara, A.Ö. Kiraz, N. Kolsuz, Synthesis and Theoretical Studies on New Amidodithiophosphonates, Journal of Molecular Structure (2016), doi: 10.1016/j.molstruc.2016.01.057. 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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ACCEPTED MANUSCRIPT Synthesis and Theoretical Studies on New Amidodithiophosphonates
Cemal Aydemir1, Mehmet Karakus1*, Izzet Kara2, Aslı Öztürk Kiraz3, Nuri Kolsuz3
Department of Chemistry, Pamukkale University, Faculty of Arts&Science, 20070, Denizli, Turkey
2
Department of Physics, Pamukkale University, Faculty of Education, 20070, Denizli, Turkey
3
Department of Physics, Pamukkale University, Faculty of Arts&Science, 20070, Denizli, Turkey
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ABSTRACT
Amidodithiophosphonates were synthesised by the reaction of 2,4-bis(4-methoxyphenyl)1,3,2,4-dithiadiphosphetane 2,4-disulfide and amines such as (-)-cis–myrtanylamine amine, (R)-(+)–1–phenylethyl amine, (S)-(-)–1–phenylethyl amine in benzene. The compounds 1-3 were characterized by elemental analyses and spectroscopically (1H-,
13
C-,
31
P-NMR). In
addition, the molecular geometry, vibrational frequencies, chemical shifts, electronic
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transition energies and thermodynamic parameters for the compound 1 were calculated by using the density functional method employing B3LYP level with different basis sets, including 6-31++G(d,p) and 6-311++G(d,p). The large HOMO-LUMO band gaps (5.08 eV and 5.06 eV, respectively) for the molecule explain the kinetic stability. The computed results
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are very close to the obtained experimental results with spectroscopic techniques.
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Keywords: Dithiophosphonate, Amidodithiophosphonate, HOMO-LUMO, B3LYP Correspondence to: Prof. Dr. Mehmet Karakus Department of Chemistry, Faculty of Arts&Sciences Pamukkale University, Kinikli, 20070 Denizli, Turkey Tel.: +90 (0) 258/2963599 Fax: +90 (0) 258/2963535 E-Mail: [email protected]
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ACCEPTED MANUSCRIPT 1. Introduction
The chemistry of dithiophosphorus compounds have been an important role in coordination chemistry as complexion reagents [1-5]. In addition, they can be used in
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agricultural and industrial fields, such as insecticides, pesticides, additives for lubricants and solvent extraction reagents for metals [6-11]. Recently, Hernandez-Galindo has been reported the
synthesis
and
characterization
of
organotelllurium(IV)
complexes
with
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ferrocenyldithiophosphponates [12]. Our research group previously reported a few studies on the synthesis and theoretical calculations of dithiophosphorus derivatives [13-14]. As a part
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of continuous studies on this area, we synthesised new amidodithiophosphonates and their theoretical properties have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods. Recently, there have been very studies on the theoretical calculations of chemical compounds due to their interesting electronic and geometrical properties in
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connection with their application [13-21]. Calculations using large basis sets are more accurate because they are less restrictive on the location of the electrons. Such calculations are also more expensive because they require computing more integrals. DFT methods account
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for electron correlation by estimating the interaction of an electron with the total electron density. DFT orbitals are formed from basis functions like those used in SCF or MP2. Most
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popular DFT method is B3LYP (Becke3-Parameter method for calculating that part of the molecular energy due to overlapping orbitals, plus the Lee-Yang-Parr method of accounting for correlation). By comparing experimental and theoretical 1H- and
13
C-NMR chemical
shifts, some practical information on the chemical structure and conformation of compounds can be obtained. The studies on chemical shift calculations based on quantum chemistry methods reveal that the geometry optimization of the molecule is an important factor to determine the chemical shifts accurately [22]. In our previous studies [13-14], we had also 2
ACCEPTED MANUSCRIPT performed for predicting the structural, vibrational and 1H- and
13
C NMR spectrum of a
derivative of dithiophosphonates by using ab initio HF and DFT calculations. Some amidodithiophosphonate derivatives have been reported in the literature [23, 24]. To our best knowledge, there are no experimental and theoretical studies on compound 1 in previous
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studies. Our aim has been understood and developed the structural and electronical properties of amidodithiophosphonate 1, due to their potential biological activity and industrial applications.
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In this study, we synthesized and characterized new amidodithiophosphonates 1-3 and they were characterized by elemental analyses, IR, 1H- NMR,
C-NMR and
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P- NMR
Beside as theoretical, we also studied on the prediction of the
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spectroscopic methods.
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geometry optimization, the vibrational frequencies, the chemical shifts, the electronic transition energies and thermal properties of the compound 1 by using B3LYP method.
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2. Experimental 2.1. Materials and instruments
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All solvents were distilled and dried by standard method before using in the reactions. Chemicals were purchased and used directly without further purification. Elemental analyses
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were performed by a GmbH vario MICRO CHNS apparatus. Melting points were measured on an Electrotermal apparatus. NMR spectra were performed in d6-DMSO on a Bruker AVANCE DRX 400 NMR spectrometer and Jeol GSX 270 in CDCl3. FT-IR spectra was done by using a Perkin-Elmer 2000 FTIR spectrophotometer (4000 – 450 cm-1 and scan’s number 4).
2.2.
(-) cis-N-myrtanyl-(4-methoxyphenyl)-amidodithiophosphonate 1
3
ACCEPTED MANUSCRIPT The reaction of 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2,4-disulfide (Lawesson’s reagent: LR) (1.00 g, 2.47 mmol) and 0.63 mL (4.94 mmol) (-)cismyrtanylamine
in
benzene
(20
mL)
resulted
in
the
formation
of
amidoferrocenyldithiophosphonate. The reaction mixture was heated with stirring at 80 oC for
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1h. After the reaction mixture was cooled to room temperature, the solution was filtered and the protected in fridge. A white crystalline product was filtered and dried in the air. Yield = 71% (1.13 g). mp 199 ̊C.
H-NMR (400.13 MHz, d6-DMSO), δ (ppm): 7.91(dd, 2H, arom.,3JP,H = 13.45 Hz, JH,H =
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8.51 Hz), 6.82(dd, 2H,arom,4JP,H = 3.52, 2JH,H = 7.15 Hz ), 3.76 (s, 3H, -OCH3), 2.91(br, 2H, -
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N-CH2-), 2.25(m, 2H, -CH2), 1.86(m, 2H, -CH2), 1.80-1.70(m, 3H, -CH, -CH2), 1.36(m, 1H, CH-), 1.064(s, 3H, -CH3), 0.78(s, 3H, -CH3). 13C-NMR (100.16 MHz, d6-DMSO), δ (ppm): 159.06(d, C4, 4JP,C= 2.90 Hz), 140.88(d, C1, 1JP,C= 109.15), 130.51(d, C2, 2JP,C= 13.02 Hz), 111.81(d, C3, 3JP,C= 13.83 Hz), 55.02(s, C5), 44.21(s, C8), 42.45(s, C7), 40.46(s, C14, C14’),
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38.76(s, C6), 32.23(s, C13), 27.49(s, C9), 25.33(s, C10), 22.76(s, C12), 18.80(s, C11). 31P-NMR (162 MHz, d6-DMSO), δ (ppm): 78.67, 65.33. IR (νmax/cm-1): 644(νasym PS2) ve 555(νsym PS2).
2.3.
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4.38; N, 4.30.
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Anal. Calcd. for C17H16NOPS2 (345.23): C, 59.15; H, 4.67; N, 4.06. Found: C, 59.93; H,
(R)-(-)-N-Phenylethyl-(4-methoxyphenyl)-amidodithiphosphonate 2
Compound 2 was prepared in the same procedure as compound 1, from [4-MeOPhPS2]2 (Lawesson’sreagent: LR) (0.50 g, 1.24 mmol) and0.31 mL (2.47 mmol) R-(-)-1phenylethylamine in benzene (20 mL). Yield = 50% (0.40 g). mp 157 oC. 1
H-NMR (400.13 MHz, d6-DMSO), δ (ppm): 7.88(dd, 2H, arom.,3JP,H = 12.85 Hz, JH,H =
8.80 Hz), 7.44(d, 2H), 7.38(m, 3H), 7.30(t, 1H), 6.82(dd, 2H, arom., 4JP,H= 2.30 Hz, JH,H = 4
ACCEPTED MANUSCRIPT 8.86 Hz), 4.22( q, 1H, -N-CH-), 3.76(s, 3H, -OCH3), 1.39(d, 3H, -CH3). 13C-NMR (100.16 MHz, d6-DMSO), δ (ppm): 161.37(s, C4), 143.7(s, C8), 141.07(d, C1, 1JP,C= 109.06), 130.53(d, C2, 2JP,C = 12.97 Hz), 128.41(s, C9), 127.36(s, C10), 126.28(s, C11), 111.80(d, C3, 3JP,C = 13.8 Hz), 55.02(s, C5), 50.29(s, C6), 23.35(s, C7). 31P-NMR (162 MHz, d6-DMSO), δ(ppm): 93.13,
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55.88. IR (νmax/cm-1): 623 (νasym PS2) ve 551 (νsym PS2). Anal. Calcd. for C15H18NOPS2 (323.22): C, 55.70; H, 5.61. Found: C, 55.93; H, 5.56.
(S)-(-)-N-Phenylethyl–(4-methoxyphenyl)-amidodithiphosphonate 3
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2. 4.
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Compound 3 was prepared in the same procedure as compound 1, from (1.00 g, 2.47 mmol) [4-MeOPhPS2]2 (Lawesson’sreagent: LR) and 0.63 mL (4.94 mmol) S-(-)-1phenylethylamine in benzene (20 mL). Yield = 69% (1.092 g). mp 164 oC. 1
H-NMR (400.13 MHz, d6-DMSO ), δ(ppm): 7.84(dd, 2H, arom.,3JP,H = 13.23 Hz, JH,H
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= 8.62Hz), 7.24(d, 2H, arom.), 7.24(m, 3H, arom.), 6.62(dd, 2H, arom., 4JP,H = 2.38 Hz, JH,H = 8.75Hz), 4.18( q, 1H, -CH-), 3.61(s, 3H, -OCH3), 1.36(d, 3H, - CH3). 13C-NMR (100.16 MHz, d6-DMSO), δ(ppm): 159.01(d, C4, 4JP,C= 2.86 Hz), 143.90(s, C8), 141.03(d, C1, 1JP,C= 109.00),
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130.51(d, C2, 2JP,C = 12.93 Hz), 128.40(s, C9), 127.35(s, C10), 126.25(s, C11), 111.79(d, C3, JP,C = 13.76 Hz), 55.01(s, C5), 50.30(s, C6), 23.44(s, C7).
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δ(ppm): 86.53, 65.20. IR (νmax/cm-1): 679(ν
asym
31
P-NMR (162 MHz, d6-DMSO),
PS2) ve 547(νsym PS2). Anal. Calcd. For
C15H18NOPS2 (323.22): C, 55.74; H, 5.61; N, 4.33. Found: C, 55.38; H, 5.77; N, 4.19. 2.5.
Theoretical Calculation We were performed quantum mechanical calculations by means of B3LYP method
with 6-31++G(d,p) and 6-311++G(d,p) basis sets to investigate the structural characteristic, the fundamental vibrational modes, the thermochemical and the electronic properties of the compound 1. Theoretical calculations were made to determine whether they are compatible with the experimental and theoretical results. In addition, thermal and electronic parameter of 5
ACCEPTED MANUSCRIPT the compound 1 was theoretically calculated. Theoretical calculations were done by using Gaussian 09.C1 program on TUBITAK clusters. GaussView 5.0.9 was used for visualization of the structure and simulated vibrational spectra [25-27]. The molecular structure of compound 1 was optimized to get the global minima of the compound 1 using B3LYP/631++G(d,p) and B3LYP/6-311++G(d,p) levels. The same calculation procedure is also used to 13
C NMR chemical shielding constants in gas phase and DMSO by
applying the GIAO-B3LYP. In order to calculate 1H- and
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predict the 1H NMR and
C NMR chemical shifts, the
integral equation formalism version of the polarizable continuum model (IEFPCM) has been used [28]. After that, the same basis set and computational method are used for the vibrational
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spectra of the compound 1 by using the optimized structure. PED calculations were performed by using VEDA 4 (Vibrational Energy Distribution Analysis) program. The scaling factor values were used in order to correct anharmonicity and neglected part of electron correlation.
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The scale factor was used as 0.96 for the frequencies [29].
Some practical information on the structure of the compound 1 has been observed by comparing experimental and theoretical vibrational data and NMR chemical shifts. We have
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also compared our theoretical results obtained by B3LYP method with our experimental data.
3. Results and Discussion
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3.1. Synthesis and Characterization
The reaction of 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane 2,4-disulfide
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(LR) with amines such as (-)-cis–myrtanylamineamine, (R)-(+)–1–phenylethyl amine, (S)-(-)– 1–phenylethyl amine in benzene were resulted in the formation of amidodithiophosphonates 1-3 (Scheme 1). The compounds 1-3 were isolated as air and moisture stable white powder and soluble in common polar solvents such as DMSO, THF, CH2Cl2. Although there are two forms (neutral and zwitter ion, see Scheme 1) observed in solution, only one form is formed in solid form [23, 24]. Both forms (neutral and zwitter ion) were confirmed by
6
31
P NMR
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Spectra. In the
P NMR spectra, there are two signals were observed in the region between
95.3 - 55.20 ppm [24]. S
S S H3CO
P
OCH 3 + 2 RNH2
P
i, ii 2 H 3CO
P
SH
S NHR
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S
S
2 H 3CO
P
S
-
3
5
H3CO
5
2
S 1
4
H3CO
P SH
14
NH
CH3
H
6
HN '
6
CH 8
9
12
9
SH
P
H3C
CH3
13
S 1
7
14
7
4
H
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2
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+NHR
8
10
11 10
11
1
2 and 3 (R- and S-isomer)
compounds 1-3.
1
H, 13C and 31P NMR Chemeical Shifts
The
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3.2.
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Scheme 1. Synthesis of compounds 1-3. i. Toluene, ii. 80-100 oC. H and C assignments for
P{1H} NMR spectra of the compounds 1-3 were measured in solution of d6-
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DMSO and observed two separate sets of signals as expected. In the 1H NMR specra of compounds 1-3, the observed signals in the range of 7.91 – 7.84 ppm and 6.82 – 6.62 ppm were attributed to the aromatic protons. The orto protons to P atom showed doublet of doublet at 7.91 ppm (dd, 2H, arom.,3JP,H = 13.45 Hz, JH,H = 8.51 Hz, for 1), 7.88 (dd, 2H, arom., 3JP,H = 12.85 Hz, JH,H = 8.80 Hz, for2), 7.84 (dd, 2H, arom., 3JP,H = 13.23 Hz, JH,H = 8.62 Hz, for 3), and meta protons to P atom were appeared at 6.82(dd, 2H, arom,4JP,H = 3.52, 2JH,H = 7.15 Hz for 1 ), 6.82 (dd, 2H, arom., 4JP,H= 2.30 Hz, JH,H = 8.86 Hz for 2) and 6.62 (dd, 2H, arom., 4
JP,H = 2.38 Hz, JH,H = 8.75Hz, for 3). 7
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13
C NMR spectra of 1-3, a doublet peak was exhibited at 140.88 ppm
(C1,1JP,C=109.15 Hz, for 1), 141.07 ppm (C1, 1JP,C= 109.06 Hz, for 2) and 141.03 ppm (C1, 1
JP,C= 109.00 Hz, for 3) due to coupling with 31P nuclei. The
31
P NMR spectrum of 1 showed two signals at 78.67 and 65.33 ppm which are
two signals in the
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assigned to zwitter ion and neutral form, respectively. The compounds 2 and 3 also showed P NMR spectrum at 93.13 and 55.88 ppm (for 2) and 86.53 and 65.20
ppm (for 3), respectively. The 1H NMR and
13
C NMR chemical shifts experimental and
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calculated values of the compound 1 was given in Tables 1.
Table 1. Theoretical NMR calculations for the compound 1.
In this study, we have presented the chemical shifts and geometric parameters of the compound 1 by using B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels. The 13
C NMR chemical shifts of the compound 1 were compared
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experimental values of 1H and
with theoretical method. The correlation parameters of the compound 1 were calculated as R2=0.9848 in gas phase, R2=0.9839 in DMSO at 6-31++G(d,p) level and R2=0.9878 in gas phase, R2=0.9871 in DMSO at 6-311++G(d,p) level. The effect of the protons in the magnetic
and
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field resulted in formidable optimization of multi-atom molecules. In addition, theoretical 1H C chemical shift values calculated with GIAO-DFT with respect to TMS of the
3.3.
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compound 1 is significantly in agreement with the experimental values.
Vibrational Analysis
The optimized geometric structure of the compound 1 with the atomic numbering scheme is given in Figure 1.
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Figure 1. The optimized theoretical geometric structure of the compound 1.
We have computed the theoretical calculation of FT-IR spectra of the compound 1 in gas
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phase by using B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels and compared them with the experimental FT-IR spectra. Our results show both the experimental and theoretical FT-IR spectra have similar results and are compatible with each other with a slight deviation
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(see Table 2 and Figure 2). The theoretical results of FT-IR spectra and assignment with TED percentage of the compound 1 obtained from B3LYP/6-31++G(d,p) level were given in Table
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2. The IR spectrum of the compounds 1-3 have characteristic vibration bands at 692-642 cm-1 and 582 – 515 cm
-1
which are attributed to ʋasym(PS2) and ʋsym(PS2), respectively. The
computed ʋasym(PS2) and ʋsym(PS2) vibrations of compound 1 were calculated in the range of 493-654 cm-1 (for 1) by B3LYP/6-31++G(d,p) level.
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Figure 2. (a) Experimental, (b) the calculated infrared spectra (FT-IR) of the compound 1 by using B3LYP/6-31++G(d,p) level. While the bonds observed at 3037 cm-1 (for 2) and a broad peak (for 1 and 3) are
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assigned to C-H aromatic stretching vibrations, the C-H aromatic stretching vibrations of
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compound 1 were calculated in the range of 3077-3099 cm-1 (for 1) by B3LYP/6-31++G(d,p). The aliphatic C-H stretching vibrations are appeared in the region of 2910-2868 cm-1. On the other hand, the calculated aliphatic C-H stretching vibrations were computed at the range of 2896-3032 cm-1 (for 1) by B3LYP/6-31++G(d,p) level. The strong bands at 1105 cm-1 (for 1), 1112 cm-1 (for 2) and 1103 cm-1 (for 3) are attributed to P-N stretching vibrations [30]. The PN stretching vibrations modes were assigned to 788-884 cm-1 (for 1) theoretically by using B3LYP/6-31++G(d,p) level. N-H stretching vibrations of compounds 1-3 are observed at 3294 cm-1, 3447 cm-1 and 3429 cm-1 respectively. In addition, the calculated N-H stretching 10
ACCEPTED MANUSCRIPT and CNH in-plane-bending values by using B3LYP/6-31++G(d,p) level were found at 3430 cm1 (for 1) and at 1378 cm1 (for 1), respectively. As a result, the experimental value of FT-IR spectra of the compound 1 was compared with both theoretical methods. The correlation (R2= 0.998) between the experimental and
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theoretical frequency values of the compound 1 are close to each other.
Table 2. Vibrational wavenumbers of the compound 1 obtained from B3LYP/6-31++G(d,p) in cm-1, experimental frequencies from FT-IR Spectra (4000 to 450 cm-1), IR
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3.4. Thermodynamic Parameters
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Intensities (km mol-1), and assignment with TED percentage in square brackets.
Thermochemical properties of the heat formation are one of the most important parameters. The heat formation values of many organic compounds are unknown. The importance of the quantum chemical calculations is increasing because of the difficulties of
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the heat effect investigations. In order to decide whether the chemical reaction will occur or not, we should check out the effects of the heat in terms of thermodynamics. The thermodynamic quantum chemical data are extensively used in the study of the organic
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compounds reaction mechanisms. Table S1 presents the calculated zero-point vibrational energies, rotational constants, entropies and dipole moment by using B3LYP/6-31++G(d,p)
3.5.
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level for the compound.
Electronic Properties
According to the molecular orbital theory; the atoms in the essential bond distance close to each other when the molecules occurring the molecule leading to the formation, s, p and d atomic orbitals mix and form orbitals belonging to the molecule. These orbitals could be considered as the places where the probability of electrons in the molecule is great [31]. The highest occupied molecular orbital energy (EHOMO) and the lowest unoccupied molecular 11
ACCEPTED MANUSCRIPT orbital energy (ELUMO) are the basis orbitals participated in the chemical reaction. The HOMO energy (πdonor) is the energy of a molecule giving an electron and the LUMO energy (πacceptor) is the energy of a molecule taking an electron [32]. The energy gap between the HOMOLUMO orbitals characterizes the electron conductivity and the spectroscopic properties of the molecules. An electronic system with a larger HOMO–LUMO gap should be less reactive
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than one having a smaller gap [33]. The HOMO-LUMO gap is high the charge transportation is not probable and the molecule is stable or non-reactive. In this study, HOMO and LUMO energies of the compound were listed in Table S2. The HOMO–LUMO gap values of the studied molecules were calculated between 5.08 and 5.06 eV in B3LYP/6-31++G(d,p) and
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B3LYP/6-311++G(d,p) levels as seen in Figure S1.
The Sum of electronic and zero-point energies of the compound was calculated between 1577.1096 (a.u.) for the compound 1 by using B3LYP/6-31++G(d,p) level. Also the chemical
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hardness (η) and the electron affinity (A) of the molecules can be calculated from the HOMOLUMO orbitals. The chemical hardness value of the compound 1 is 2.54 eV and 2.53 eV. The electron affinity (A), the electronegativity (χ) and the chemical softness (S) of the molecules were given in Table S2.
The ESP (Electrostatic Surface Potential) that associated with partial charge and
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electronegativity and MEP (Molecular Electrostatic Potential) plots exhibit the distribution of charge of compounds with respect to the difference between positive and negative charge [32]. The MEP map of the surface presented in molecular size also shows the shape and electrostatic potential value. The different colors in the MEP surfaces show different values of
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the electrostatic potentials. In the MEP map red regions show the negative potentials, rich electron regions and blue regions show the positive potentials poor electron regions [34]. The
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deepest blue defines strongest attraction and the deepest red describes strongest repulsion. In the MEP of the compound 1 potential change from -0.04323 a.u. to 0.04323 a.u. as seen from Figure S2.
For the compounds 1 the red-orange regions seen over the sulphur atom so the compound 1 shows nucleophilic reactivity property because of the electron density on the sulphur atoms. A density of states diagram of the molecular orbital of the compounds 1 is shown in Figure S3. This graph was drawn by Gausssum2.1 [35]. The NBO analysis reveal that the bond strength, proton affinity and position of O–C, CC, C-P, N-P groups have major influence on the reactivity of considered molecules [36]. 12
ACCEPTED MANUSCRIPT Table S3 shows the intramolecular, rehybridization and delocalization of electron density (ED) of the compound 1. Both compounds; in the σ (C7-C9) bond C7 bond hybrid of the C7C9 bond gains 36.01% and 35.95% in s character and 63.96% and 64.01% in p character (with hybrid orbital sp1.78 and sp1.78). For the compound 1, C6-C8 bond has σ bond C6 bond
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hybrid of the C6-C8 bond gains 38.11% in s character and 61.85% in p character.
4. Conclusion
Amidodithiophosphonates 1-3 were synthesized and characterized by elemental 13
C- and
31
P- NMR spectroscopy. The molecular structures of the
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analyses, IR, 1H-,
compound 1 have been studied by using the ab initio calculations method based on B3LYP.
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The experimental and theoretical calculations on vibrational frequencies, 1H-NMR and
13
C-
NMR spectra are very close to each other. Highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) of the compound 1 have been predicted. In addition, the thermodynamic parameters such as total thermal energy, entropy, heat capacity,
Acknowledgements
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thermal enthalpies and thermal free energies values of the molecules were calculated.
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This study was supported by Pamukkale University (Grant no: 2009FBE020 and
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2012BSP004). Computation has been performed using TUBITAK/ULAKBIM clusters.
References
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ACCEPTED MANUSCRIPT [3] A. Mesparo, I. Kani, A.A. Mohammed, M.A. Omary, J.P. Fackler, Jr, Syntheses and Structures of Dinuclear Gold(I) Dithiophosphonate Complexes and the Reaction of the Dithiophosphonate Complexes with Phosphines: Diverse Coordination Types, Inorg. Chem. 42 (2003) 5311-5319. [4] W.E. Van Zyl, R.J. Staples, Jr. J.P. Fackler, Dinuclear gold(I) dithiophosphonate complexes: formation, structure and reactivity, Inorg. Chem. Comm. 1 (1998) 51-54.
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[7] M.C. Aragoni, M. Arca, F. Demartin, F.A. Devillanova, C. Graiff, F. Isaia, V. Lippolis, A. Tiripicchio, G. Verani, Reactivity of phosphonodithioato Ni-II complexes: solution equilibria, solid state studies and theoretical calculations on the adduct formation with some pyridine derivatives, J. Chem. Soc. Dalton Trans. (2001) 2671-2677. [8] E.G. Saglam, A. Ebinç, C. T. Zeyrek, H. Unver, T. Hokelek, Structural studies on some dithiophosphonato complexes of Ni(II), Cd(II), Hg(II) and theoretical studies on a dithiophosphonato Ni(II) complex using density functional theory, J. Mol. Struct. 1099 (2015) 490-501.
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[10] E. Alberti, G.A. Ardizzoia, S. Brenna, F. Castelli, S. Gali, A. Maspero,, The synthesis of a new dithiophosphonic acid and its coordination properties toward Ni(II): A combined NMR and X-ray diffraction study, Polyhedron 26 (2007) 958-966.
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[11] G. Saglam, E. O. Celik, H. Yilmaz, N. Acar, Synthesis and Spectroscopic Characterization of Novel Aryldithiofluorophosphonate Derivatives and X-Ray Studies of [(4-CH3OC6H4)(F)P(S)S-][PH4P+], Phosphorus, Sulfur, Silicon and Relat. Elem. 187 (2012) 1339-1346. [12] M.D.C. Hernandez-Galindo, M. Moya-Cabrera, V. Jancik, R.A. Toscano, R. CeaOlivares, Synthesis and structural characterization of organotellurium(IV) complexes bearing ferrocenyldithiophosphonate ligands. The first examples of tellurium dithiophosphonates, J. Organomet. Chem. 280 (2014) 772-773. [13] M. Karakus, S. Solak, T. Hökelek, H. Dal, A. Bayrakdar, S. Özdemir Kart, M. Karabacak, H.H. Kart, Synthesis, crystal structure and ab initio/DFT calculations of a derivative of dithiophosphonates, Spectrochim. Acta Part A 122 (2014) 582–590. [14] H.H. Kart, S. Özdemir Kart, M. Karakus, M. Kurt, Ab initio/DFT calculations of tertbutyl ammonium salt of O,O'-dibornyl dithiophosphate, Spectrochim. Acta Part A 129 (2014) 421-428. 14
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[18] M. Karabacak, A. Coruh, M. Kurt, FT-IR, FT-Raman, NMR spectra, and molecular structure investigation of 2,3 Dibromo-N-Methylmaleimide: A combined experimental and theoretical study, J. Mol. Struct. 892 (2008) 125–131. [19] C. Lee, W. Yang, R.G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B37 (1988) 785-789.
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[23] V.G. Albano, M.C. Aragoni, M. Arca, C. Castellari, F. Demartin, F. Isaia, V. Lippolis, L. Loddo, G. Verani, An unprecedented example of a cis-phosphonodithioato nickel(II) complex built by an extensive hydrogen bonding supramolecular network, Chem. Commun. (2002) 1170-1171.
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[24] M. Karakus, Synthesis and Characterization of Chiral Gold(I) Phosphine Complexes with New Dithiophosphorus Ligands, Phosphorus, Sulfur Silicon Relat. Elem. 186 (2011) 1523-1530. [25] J. B. Foresman A. E. Frisch (1996) Exploring Chemistry with Electronic Structure Methods, Gaussian Inc. [26] Gaussian 09, Revision C.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, 15
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[36] M. T. Tari, N. Ahmadinejad, Theoretical N-14 and O-17 nuclear quadrupole resonance parameters for tirapazamine and related metabolites, Struct. Chem. 25, (2014) 1281-1287.
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ACCEPTED MANUSCRIPT Table Captions Table 1. Theoretical NMR calculations for the compound 1. Table 2. Vibrational wavenumbers of the compound 1 obtained from B3LYP/6-31++G(d,p) in cm-1, experimental frequencies from FT-IR Spectra (4000 to 450 cm-1), IR
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Intensities (km mol-1), and assignment with TED percentage in square brackets. Table S1. Calculated thermodynamic parameters of the compound 1. Table S2. Electronic parameters of the compound 1.
Table S3. The hybrids of selected natural bond orbitals calculated by NBO analysis for the
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compound 1 by using B3LYP/6-31++G(d,p) level.
Table 1. Theoretical NMR calculations for the compound 1. Atom number Exp. 6-C 159.06
Gas phase 6-31++ G(d,p) 159.64
DMSO
6-311++ G(d,p) 170.8109
17
6-31++G(d,p) 160.69
6-311++ G(d,p) 171.97
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12-H 4-H 3-H 2-H 33-H 32-H 48-H 39-H 34-H 28-H 21-H 31-H 36-H 30-H 26-H 46-H 42-H 35-H 45-H 47-H 43-H 38-H 41-H
6.82 6.82 3.76 3.76 3.76 2.91 1.5 1.8 1.8 1.7 2.91 1.36 2.25 2.25 1.86 1.06 1.06
140.90 138.20 133.84 124.00 115.30 57.42 52.86
46.90 46.70 46.27 45.97 37.65 30.17
47.3675 48.4767 47.0063 45.9688 37.242 31.6523
46.90 46.52 46.14 46.14 37.15 30.00
48.26 47.33 46.85 46.10 36.71 31.48
28.94 24.79 24.15 8.36 7.88 7.15
29.8268 25.2687 24.4298 8.4364 7.8579 7.159
28.52 24.30 23.78 8.37 7.95 7.28
6.92 4.16 3.77 3.74 3.19 2.63
6.8549 4.0703 3.6744 3.6744 3.1776 2.7166
7.27 4.27 3.93 3.93 3.20 2.88
7.19 4.19 3.87 3.84 3.19 2.96
2.7154 2.4945 2.441 2.2296 2.1471 1.8779
2.87 2.53 2.43 2.33 2.20 2.02
2.95 2.50 2.51 2.28 2.21 1.88
2.01 1.92 1.80 1.70 1.41 1.21
1.991 1.9173 1.7496 1.66 1.3759 1.2008
2.02 1.94 1.85 1.70 1.44 1.25
2.00 1.93 1.80 1.67 1.40 1.25
1.08 0.99 0.99 0.86 0.81
1.158 1.1342 1.0109 0.9566 0.8521
1.08 1.00 0.98 0.88 0.80
1.15 1.13 1.01 0.98 0.84
2.60 2.53 2.36 2.28 2.14 2.01
1.86 1.06 0.78 0.78 1.8 0.78
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130.59 127.04 125.64 115.48 107.24 54.71 50.96
29.37 24.78 24.02 8.45 7.93 7.28
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27.49 18.8 18.8 32.23 7.91 7.91
140.8236 138.2808 135.2097 123.747 113.1921 56.7122 52.8887
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44-C 40-C 23-C 15-H 14-H 10-H
44.21 38.76 42.45 40.46 22.76 25.33
130.56 127.15 126.92 115.20 105.36 53.97 50.97
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29-C 22-C 24-C 27-C 37-C 25-C
130.51 130.51 140.88 111.81 111.81 55.02
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9-C 13-C 7-C 8-C 1-C 20-C
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11-C
Table 2. Vibrational wavenumbers of the compound 1 obtained from B3LYP/6-31++G(d,p) in cm-1, experimental frequencies from FT-IR Spectra (4000 to 450 cm-1), IR Intensities (km mol-1), and assignment with TED percentage in square brackets.
18
ACCEPTED MANUSCRIPT Mode no.
Ir Exp 5.09
Unscaled
Scaled
Assignment [TED]≥10% a
317
ʋSP(38)
27
393
377
δCPN(16)
30
0.01
423
406
τHCCCring(79)
32
38.37
455
437
ʋPC(13) + ʋSP(10)
33
23.68
509
489
δCOC(15)
34
25.19
511
491
ʋPS
35
18.58
532
511
τHCOC(42) + ωCHring
38
25.82
617
592
ʋasymPS
644
618
δCCCring
678
651
δHSP(12) + ʋasymPS
731
702
τHCCCring(57)
817
784
ʋCC(37) + τHCCC(13) + ʋPN
831
798
δHSP(13) + τHCCC(23)
555 PS2 sym 555 PS2 sym 644 PS2 asym
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330
1.3
23
4.25
42
93.33
43
2.12
47
25.37
49
20.15
50
15.84
826 PN
849
815
τHCCO(30) + ʋPN + ωCHring
51
59.01
826 PN
852
818
τHCCO(13) + ʋPN + ωCHring
52
3.16
53
29.49
55
2.72
56
2.27
57
2.12
58
0.89
60
0.92
61
7.17
62
0.94
63
0.76
65
4.17
66
49.78
67
118.3
69
17.17
70
121.1
71
0.21
826 PN
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644 PS2 asym
SC
40
876
841
ʋCC(19)
884
849
ʋPN + ρHCC
932
895
ʋCC(33)
952
914
ʋCC(15)
966
927
δHCC(13)
969
930
τHCCC(10) + τHCCH(67)
990
950
τHCCH(12) + τHCCO(18)
1006
966
δHCC(18)
1019
978
δHCC(26)
1023
982
δCCC + δHCC
1051
1009
ʋCC(29)
1253 CO
1060
1018
ʋCC(10) + ʋOC(73)
1105 CN
1086
1043
ʋNC(64)
1118
1073
ʋCC(18)
1119
1074
ʋCC(12) + ʋPC(19)
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826 PN
1092
ʋCC(15)
1140
1094
δHCHring(15) + ʋCCring(21)
12.93
1171
1124
δHCH(83) + ʋCC(14)
7.47
1205
1157
δHCH(30) + δHCO(10)
60.95
1208
1160
δHCO(60) + ʋCCring(12)
0.69
1212
1164
δHCC(46)
79
0.35
1225
1176
δHCC(28)
80
1.28
1232
1183
ʋCC(11)
81
8.15
1245
1195
δHCN(30)
83
20.28
1271
1220
δHCN(42)
84
288.5
1294
1242
ʋCCring(51) + ʋCOring + δHCCring
85
2.94
1296
1244
δHCC(33)
87
1.51
1319
1266
δHCC(50)
72 74 76 77 78
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1137
5.83
1253 CO
19
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1329
1276
δHCCring(65)
89
5.02
1344
1290
δHCC(31) + τCH2
90
1348
1294
ʋCCring(56)
91
47.4 1467 C=C aromatic 2.21
1361
1307
δHCC(33) + τCH2
92
3.48
1380
1325
δρHCC(29)
93
1.73
1381
1326
δHCH(10)
94
3.82
1401
1345
δHNP(33)
95
5.96
1409
1353
δHCC(34)
96
9.5
1429
1372
δHCH(56) + ωCH3
97
68.21
1435
1378
δCNH(48)
98
18.66 1467 C=C aromatic 12.69
1445
1387
δHCHring(26) + ʋCCring
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88
1421
δHCH(71)
2.17
1490
1430
δHCH(72)
101
2.29
1491
1431
δHCH(69)
102
0.24
1498
1438
δHCH(70)
103
8.72
1499
1439
δHCH(98)
104
11.94
1506
1446
δHCH(63)
105
43.44
1508
1448
δHCH(69)
106
5.82
1513
1452
δHCH(64)
107
11.31
1520
1459
δHCH(64)
108
10.48
1521
1460
δHCH(59)
109
5.09
1529
1468
δHCH(74)
110
90.85
1536
1475
δHCH(38) + ʋCCring
111
28.48 1594 C=C aromatic 172.4 1594 C=C aromatic
1608
1544
δHCCring(11) + ʋCCring(68)+ δCNH
1645
1579
ʋCCring(61) + δHCCring
2701
2593
ʋSH(100)
3017
2896
ʋCH(90)
3024
2903
ʋsymCH3(91)
3028
2907
ʋsymCH3(88)
3030
2909
ʋCH(87)
3033
2912
ʋsymCH(89)
112
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99
SC
1480
100
113
1.24
114
9.51
115
62.73
116
14.97
117
25.78
118
44.61
119
76.86
3038
2916
ʋCH(91)
120
22.87
3043
2921
ʋCH(86)
121
81.54
3049
2927
ʋCH(86)
122
40.26
3052
2930
ʋCH(87)
123
37.74
3060
2938
ʋCH(77)
124
16.02
3063
2940
ʋCH(82)
125
9.9
3082
2959
ʋasymCH3(91)
127
82.06
3088
2964
ʋasymCH2(82)
128
26.8
3090
2966
ʋasymCH3(94)
130
23.21
3118
2993
ʋCH(85)
131
44.5
3133
3008
ʋCH(88)
132
26.46
3148
3022
ʋasymCH3(91)
133
20.22
3158
3032
ʋCH(91)
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2911 C-H alipatic
20
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1.33
3205
3077
ʋasymCHring(92)
135
0.19
3207
3079
ʋCH(93)
136
5.35
3219
3090
ʋCH(98)
137
8.96
3228
3099
ʋCH(98)
2983 C-H aromatic
32.06
3294 N-H 3573 3430 ʋNH(100 a TED: Total Energy Distribution, ʋ; stretching, δ; in-plane-bending, τ; torsion, ρ; rocking, ω; wagging, sym; 138
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symmetric, asym; asymmetric.
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ACCEPTED MANUSCRIPT HIGHLIGHTS
1. New amidodithiophosphonates were synthesized. 2. All compounds were characterized by IR,NMR(H-, 13C and 31P) spectroscopic
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methods. 3. IR, 1H NMR and 13C NMR of the compound 1 were computed using B3LYP method.
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4. The HOMO, LUMO energy gap of the compound 1 were theoretically calculated.
S0022-2860(16)30057-6
DOI:
10.1016/j.molstruc.2016.01.057
Reference:
MOLSTR 22173
To appear in:
Journal of Molecular Structure
Received Date: 8 December 2015 Revised Date:
22 January 2016
Accepted Date: 22 January 2016
Please cite this article as: C. Aydemir, M. Karakus, I. Kara, A.Ö. Kiraz, N. Kolsuz, Synthesis and Theoretical Studies on New Amidodithiophosphonates, Journal of Molecular Structure (2016), doi: 10.1016/j.molstruc.2016.01.057. 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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ACCEPTED MANUSCRIPT Synthesis and Theoretical Studies on New Amidodithiophosphonates
Cemal Aydemir1, Mehmet Karakus1*, Izzet Kara2, Aslı Öztürk Kiraz3, Nuri Kolsuz3
Department of Chemistry, Pamukkale University, Faculty of Arts&Science, 20070, Denizli, Turkey
2
Department of Physics, Pamukkale University, Faculty of Education, 20070, Denizli, Turkey
3
Department of Physics, Pamukkale University, Faculty of Arts&Science, 20070, Denizli, Turkey
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1
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ABSTRACT
Amidodithiophosphonates were synthesised by the reaction of 2,4-bis(4-methoxyphenyl)1,3,2,4-dithiadiphosphetane 2,4-disulfide and amines such as (-)-cis–myrtanylamine amine, (R)-(+)–1–phenylethyl amine, (S)-(-)–1–phenylethyl amine in benzene. The compounds 1-3 were characterized by elemental analyses and spectroscopically (1H-,
13
C-,
31
P-NMR). In
addition, the molecular geometry, vibrational frequencies, chemical shifts, electronic
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transition energies and thermodynamic parameters for the compound 1 were calculated by using the density functional method employing B3LYP level with different basis sets, including 6-31++G(d,p) and 6-311++G(d,p). The large HOMO-LUMO band gaps (5.08 eV and 5.06 eV, respectively) for the molecule explain the kinetic stability. The computed results
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are very close to the obtained experimental results with spectroscopic techniques.
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Keywords: Dithiophosphonate, Amidodithiophosphonate, HOMO-LUMO, B3LYP Correspondence to: Prof. Dr. Mehmet Karakus Department of Chemistry, Faculty of Arts&Sciences Pamukkale University, Kinikli, 20070 Denizli, Turkey Tel.: +90 (0) 258/2963599 Fax: +90 (0) 258/2963535 E-Mail: [email protected]
1
ACCEPTED MANUSCRIPT 1. Introduction
The chemistry of dithiophosphorus compounds have been an important role in coordination chemistry as complexion reagents [1-5]. In addition, they can be used in
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agricultural and industrial fields, such as insecticides, pesticides, additives for lubricants and solvent extraction reagents for metals [6-11]. Recently, Hernandez-Galindo has been reported the
synthesis
and
characterization
of
organotelllurium(IV)
complexes
with
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ferrocenyldithiophosphponates [12]. Our research group previously reported a few studies on the synthesis and theoretical calculations of dithiophosphorus derivatives [13-14]. As a part
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of continuous studies on this area, we synthesised new amidodithiophosphonates and their theoretical properties have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods. Recently, there have been very studies on the theoretical calculations of chemical compounds due to their interesting electronic and geometrical properties in
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connection with their application [13-21]. Calculations using large basis sets are more accurate because they are less restrictive on the location of the electrons. Such calculations are also more expensive because they require computing more integrals. DFT methods account
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for electron correlation by estimating the interaction of an electron with the total electron density. DFT orbitals are formed from basis functions like those used in SCF or MP2. Most
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popular DFT method is B3LYP (Becke3-Parameter method for calculating that part of the molecular energy due to overlapping orbitals, plus the Lee-Yang-Parr method of accounting for correlation). By comparing experimental and theoretical 1H- and
13
C-NMR chemical
shifts, some practical information on the chemical structure and conformation of compounds can be obtained. The studies on chemical shift calculations based on quantum chemistry methods reveal that the geometry optimization of the molecule is an important factor to determine the chemical shifts accurately [22]. In our previous studies [13-14], we had also 2
ACCEPTED MANUSCRIPT performed for predicting the structural, vibrational and 1H- and
13
C NMR spectrum of a
derivative of dithiophosphonates by using ab initio HF and DFT calculations. Some amidodithiophosphonate derivatives have been reported in the literature [23, 24]. To our best knowledge, there are no experimental and theoretical studies on compound 1 in previous
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studies. Our aim has been understood and developed the structural and electronical properties of amidodithiophosphonate 1, due to their potential biological activity and industrial applications.
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In this study, we synthesized and characterized new amidodithiophosphonates 1-3 and they were characterized by elemental analyses, IR, 1H- NMR,
C-NMR and
31
P- NMR
Beside as theoretical, we also studied on the prediction of the
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spectroscopic methods.
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geometry optimization, the vibrational frequencies, the chemical shifts, the electronic transition energies and thermal properties of the compound 1 by using B3LYP method.
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2. Experimental 2.1. Materials and instruments
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All solvents were distilled and dried by standard method before using in the reactions. Chemicals were purchased and used directly without further purification. Elemental analyses
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were performed by a GmbH vario MICRO CHNS apparatus. Melting points were measured on an Electrotermal apparatus. NMR spectra were performed in d6-DMSO on a Bruker AVANCE DRX 400 NMR spectrometer and Jeol GSX 270 in CDCl3. FT-IR spectra was done by using a Perkin-Elmer 2000 FTIR spectrophotometer (4000 – 450 cm-1 and scan’s number 4).
2.2.
(-) cis-N-myrtanyl-(4-methoxyphenyl)-amidodithiophosphonate 1
3
ACCEPTED MANUSCRIPT The reaction of 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2,4-disulfide (Lawesson’s reagent: LR) (1.00 g, 2.47 mmol) and 0.63 mL (4.94 mmol) (-)cismyrtanylamine
in
benzene
(20
mL)
resulted
in
the
formation
of
amidoferrocenyldithiophosphonate. The reaction mixture was heated with stirring at 80 oC for
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1h. After the reaction mixture was cooled to room temperature, the solution was filtered and the protected in fridge. A white crystalline product was filtered and dried in the air. Yield = 71% (1.13 g). mp 199 ̊C.
H-NMR (400.13 MHz, d6-DMSO), δ (ppm): 7.91(dd, 2H, arom.,3JP,H = 13.45 Hz, JH,H =
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1
8.51 Hz), 6.82(dd, 2H,arom,4JP,H = 3.52, 2JH,H = 7.15 Hz ), 3.76 (s, 3H, -OCH3), 2.91(br, 2H, -
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N-CH2-), 2.25(m, 2H, -CH2), 1.86(m, 2H, -CH2), 1.80-1.70(m, 3H, -CH, -CH2), 1.36(m, 1H, CH-), 1.064(s, 3H, -CH3), 0.78(s, 3H, -CH3). 13C-NMR (100.16 MHz, d6-DMSO), δ (ppm): 159.06(d, C4, 4JP,C= 2.90 Hz), 140.88(d, C1, 1JP,C= 109.15), 130.51(d, C2, 2JP,C= 13.02 Hz), 111.81(d, C3, 3JP,C= 13.83 Hz), 55.02(s, C5), 44.21(s, C8), 42.45(s, C7), 40.46(s, C14, C14’),
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38.76(s, C6), 32.23(s, C13), 27.49(s, C9), 25.33(s, C10), 22.76(s, C12), 18.80(s, C11). 31P-NMR (162 MHz, d6-DMSO), δ (ppm): 78.67, 65.33. IR (νmax/cm-1): 644(νasym PS2) ve 555(νsym PS2).
2.3.
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4.38; N, 4.30.
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Anal. Calcd. for C17H16NOPS2 (345.23): C, 59.15; H, 4.67; N, 4.06. Found: C, 59.93; H,
(R)-(-)-N-Phenylethyl-(4-methoxyphenyl)-amidodithiphosphonate 2
Compound 2 was prepared in the same procedure as compound 1, from [4-MeOPhPS2]2 (Lawesson’sreagent: LR) (0.50 g, 1.24 mmol) and0.31 mL (2.47 mmol) R-(-)-1phenylethylamine in benzene (20 mL). Yield = 50% (0.40 g). mp 157 oC. 1
H-NMR (400.13 MHz, d6-DMSO), δ (ppm): 7.88(dd, 2H, arom.,3JP,H = 12.85 Hz, JH,H =
8.80 Hz), 7.44(d, 2H), 7.38(m, 3H), 7.30(t, 1H), 6.82(dd, 2H, arom., 4JP,H= 2.30 Hz, JH,H = 4
ACCEPTED MANUSCRIPT 8.86 Hz), 4.22( q, 1H, -N-CH-), 3.76(s, 3H, -OCH3), 1.39(d, 3H, -CH3). 13C-NMR (100.16 MHz, d6-DMSO), δ (ppm): 161.37(s, C4), 143.7(s, C8), 141.07(d, C1, 1JP,C= 109.06), 130.53(d, C2, 2JP,C = 12.97 Hz), 128.41(s, C9), 127.36(s, C10), 126.28(s, C11), 111.80(d, C3, 3JP,C = 13.8 Hz), 55.02(s, C5), 50.29(s, C6), 23.35(s, C7). 31P-NMR (162 MHz, d6-DMSO), δ(ppm): 93.13,
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55.88. IR (νmax/cm-1): 623 (νasym PS2) ve 551 (νsym PS2). Anal. Calcd. for C15H18NOPS2 (323.22): C, 55.70; H, 5.61. Found: C, 55.93; H, 5.56.
(S)-(-)-N-Phenylethyl–(4-methoxyphenyl)-amidodithiphosphonate 3
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2. 4.
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Compound 3 was prepared in the same procedure as compound 1, from (1.00 g, 2.47 mmol) [4-MeOPhPS2]2 (Lawesson’sreagent: LR) and 0.63 mL (4.94 mmol) S-(-)-1phenylethylamine in benzene (20 mL). Yield = 69% (1.092 g). mp 164 oC. 1
H-NMR (400.13 MHz, d6-DMSO ), δ(ppm): 7.84(dd, 2H, arom.,3JP,H = 13.23 Hz, JH,H
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= 8.62Hz), 7.24(d, 2H, arom.), 7.24(m, 3H, arom.), 6.62(dd, 2H, arom., 4JP,H = 2.38 Hz, JH,H = 8.75Hz), 4.18( q, 1H, -CH-), 3.61(s, 3H, -OCH3), 1.36(d, 3H, - CH3). 13C-NMR (100.16 MHz, d6-DMSO), δ(ppm): 159.01(d, C4, 4JP,C= 2.86 Hz), 143.90(s, C8), 141.03(d, C1, 1JP,C= 109.00),
3
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130.51(d, C2, 2JP,C = 12.93 Hz), 128.40(s, C9), 127.35(s, C10), 126.25(s, C11), 111.79(d, C3, JP,C = 13.76 Hz), 55.01(s, C5), 50.30(s, C6), 23.44(s, C7).
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δ(ppm): 86.53, 65.20. IR (νmax/cm-1): 679(ν
asym
31
P-NMR (162 MHz, d6-DMSO),
PS2) ve 547(νsym PS2). Anal. Calcd. For
C15H18NOPS2 (323.22): C, 55.74; H, 5.61; N, 4.33. Found: C, 55.38; H, 5.77; N, 4.19. 2.5.
Theoretical Calculation We were performed quantum mechanical calculations by means of B3LYP method
with 6-31++G(d,p) and 6-311++G(d,p) basis sets to investigate the structural characteristic, the fundamental vibrational modes, the thermochemical and the electronic properties of the compound 1. Theoretical calculations were made to determine whether they are compatible with the experimental and theoretical results. In addition, thermal and electronic parameter of 5
ACCEPTED MANUSCRIPT the compound 1 was theoretically calculated. Theoretical calculations were done by using Gaussian 09.C1 program on TUBITAK clusters. GaussView 5.0.9 was used for visualization of the structure and simulated vibrational spectra [25-27]. The molecular structure of compound 1 was optimized to get the global minima of the compound 1 using B3LYP/631++G(d,p) and B3LYP/6-311++G(d,p) levels. The same calculation procedure is also used to 13
C NMR chemical shielding constants in gas phase and DMSO by
applying the GIAO-B3LYP. In order to calculate 1H- and
13
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predict the 1H NMR and
C NMR chemical shifts, the
integral equation formalism version of the polarizable continuum model (IEFPCM) has been used [28]. After that, the same basis set and computational method are used for the vibrational
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spectra of the compound 1 by using the optimized structure. PED calculations were performed by using VEDA 4 (Vibrational Energy Distribution Analysis) program. The scaling factor values were used in order to correct anharmonicity and neglected part of electron correlation.
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The scale factor was used as 0.96 for the frequencies [29].
Some practical information on the structure of the compound 1 has been observed by comparing experimental and theoretical vibrational data and NMR chemical shifts. We have
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also compared our theoretical results obtained by B3LYP method with our experimental data.
3. Results and Discussion
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3.1. Synthesis and Characterization
The reaction of 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane 2,4-disulfide
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(LR) with amines such as (-)-cis–myrtanylamineamine, (R)-(+)–1–phenylethyl amine, (S)-(-)– 1–phenylethyl amine in benzene were resulted in the formation of amidodithiophosphonates 1-3 (Scheme 1). The compounds 1-3 were isolated as air and moisture stable white powder and soluble in common polar solvents such as DMSO, THF, CH2Cl2. Although there are two forms (neutral and zwitter ion, see Scheme 1) observed in solution, only one form is formed in solid form [23, 24]. Both forms (neutral and zwitter ion) were confirmed by
6
31
P NMR
ACCEPTED MANUSCRIPT 31
Spectra. In the
P NMR spectra, there are two signals were observed in the region between
95.3 - 55.20 ppm [24]. S
S S H3CO
P
OCH 3 + 2 RNH2
P
i, ii 2 H 3CO
P
SH
S NHR
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S
S
2 H 3CO
P
S
-
3
5
H3CO
5
2
S 1
4
H3CO
P SH
14
NH
CH3
H
6
HN '
6
CH 8
9
12
9
SH
P
H3C
CH3
13
S 1
7
14
7
4
H
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3
2
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+NHR
8
10
11 10
11
1
2 and 3 (R- and S-isomer)
compounds 1-3.
1
H, 13C and 31P NMR Chemeical Shifts
The
31
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3.2.
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Scheme 1. Synthesis of compounds 1-3. i. Toluene, ii. 80-100 oC. H and C assignments for
P{1H} NMR spectra of the compounds 1-3 were measured in solution of d6-
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DMSO and observed two separate sets of signals as expected. In the 1H NMR specra of compounds 1-3, the observed signals in the range of 7.91 – 7.84 ppm and 6.82 – 6.62 ppm were attributed to the aromatic protons. The orto protons to P atom showed doublet of doublet at 7.91 ppm (dd, 2H, arom.,3JP,H = 13.45 Hz, JH,H = 8.51 Hz, for 1), 7.88 (dd, 2H, arom., 3JP,H = 12.85 Hz, JH,H = 8.80 Hz, for2), 7.84 (dd, 2H, arom., 3JP,H = 13.23 Hz, JH,H = 8.62 Hz, for 3), and meta protons to P atom were appeared at 6.82(dd, 2H, arom,4JP,H = 3.52, 2JH,H = 7.15 Hz for 1 ), 6.82 (dd, 2H, arom., 4JP,H= 2.30 Hz, JH,H = 8.86 Hz for 2) and 6.62 (dd, 2H, arom., 4
JP,H = 2.38 Hz, JH,H = 8.75Hz, for 3). 7
ACCEPTED MANUSCRIPT In the
13
C NMR spectra of 1-3, a doublet peak was exhibited at 140.88 ppm
(C1,1JP,C=109.15 Hz, for 1), 141.07 ppm (C1, 1JP,C= 109.06 Hz, for 2) and 141.03 ppm (C1, 1
JP,C= 109.00 Hz, for 3) due to coupling with 31P nuclei. The
31
P NMR spectrum of 1 showed two signals at 78.67 and 65.33 ppm which are
two signals in the
31
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assigned to zwitter ion and neutral form, respectively. The compounds 2 and 3 also showed P NMR spectrum at 93.13 and 55.88 ppm (for 2) and 86.53 and 65.20
ppm (for 3), respectively. The 1H NMR and
13
C NMR chemical shifts experimental and
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calculated values of the compound 1 was given in Tables 1.
Table 1. Theoretical NMR calculations for the compound 1.
In this study, we have presented the chemical shifts and geometric parameters of the compound 1 by using B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels. The 13
C NMR chemical shifts of the compound 1 were compared
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experimental values of 1H and
with theoretical method. The correlation parameters of the compound 1 were calculated as R2=0.9848 in gas phase, R2=0.9839 in DMSO at 6-31++G(d,p) level and R2=0.9878 in gas phase, R2=0.9871 in DMSO at 6-311++G(d,p) level. The effect of the protons in the magnetic
and
13
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field resulted in formidable optimization of multi-atom molecules. In addition, theoretical 1H C chemical shift values calculated with GIAO-DFT with respect to TMS of the
3.3.
AC C
compound 1 is significantly in agreement with the experimental values.
Vibrational Analysis
The optimized geometric structure of the compound 1 with the atomic numbering scheme is given in Figure 1.
8
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ACCEPTED MANUSCRIPT
Figure 1. The optimized theoretical geometric structure of the compound 1.
We have computed the theoretical calculation of FT-IR spectra of the compound 1 in gas
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phase by using B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels and compared them with the experimental FT-IR spectra. Our results show both the experimental and theoretical FT-IR spectra have similar results and are compatible with each other with a slight deviation
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(see Table 2 and Figure 2). The theoretical results of FT-IR spectra and assignment with TED percentage of the compound 1 obtained from B3LYP/6-31++G(d,p) level were given in Table
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2. The IR spectrum of the compounds 1-3 have characteristic vibration bands at 692-642 cm-1 and 582 – 515 cm
-1
which are attributed to ʋasym(PS2) and ʋsym(PS2), respectively. The
computed ʋasym(PS2) and ʋsym(PS2) vibrations of compound 1 were calculated in the range of 493-654 cm-1 (for 1) by B3LYP/6-31++G(d,p) level.
9
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ACCEPTED MANUSCRIPT
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Figure 2. (a) Experimental, (b) the calculated infrared spectra (FT-IR) of the compound 1 by using B3LYP/6-31++G(d,p) level. While the bonds observed at 3037 cm-1 (for 2) and a broad peak (for 1 and 3) are
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assigned to C-H aromatic stretching vibrations, the C-H aromatic stretching vibrations of
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compound 1 were calculated in the range of 3077-3099 cm-1 (for 1) by B3LYP/6-31++G(d,p). The aliphatic C-H stretching vibrations are appeared in the region of 2910-2868 cm-1. On the other hand, the calculated aliphatic C-H stretching vibrations were computed at the range of 2896-3032 cm-1 (for 1) by B3LYP/6-31++G(d,p) level. The strong bands at 1105 cm-1 (for 1), 1112 cm-1 (for 2) and 1103 cm-1 (for 3) are attributed to P-N stretching vibrations [30]. The PN stretching vibrations modes were assigned to 788-884 cm-1 (for 1) theoretically by using B3LYP/6-31++G(d,p) level. N-H stretching vibrations of compounds 1-3 are observed at 3294 cm-1, 3447 cm-1 and 3429 cm-1 respectively. In addition, the calculated N-H stretching 10
ACCEPTED MANUSCRIPT and CNH in-plane-bending values by using B3LYP/6-31++G(d,p) level were found at 3430 cm1 (for 1) and at 1378 cm1 (for 1), respectively. As a result, the experimental value of FT-IR spectra of the compound 1 was compared with both theoretical methods. The correlation (R2= 0.998) between the experimental and
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theoretical frequency values of the compound 1 are close to each other.
Table 2. Vibrational wavenumbers of the compound 1 obtained from B3LYP/6-31++G(d,p) in cm-1, experimental frequencies from FT-IR Spectra (4000 to 450 cm-1), IR
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3.4. Thermodynamic Parameters
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Intensities (km mol-1), and assignment with TED percentage in square brackets.
Thermochemical properties of the heat formation are one of the most important parameters. The heat formation values of many organic compounds are unknown. The importance of the quantum chemical calculations is increasing because of the difficulties of
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the heat effect investigations. In order to decide whether the chemical reaction will occur or not, we should check out the effects of the heat in terms of thermodynamics. The thermodynamic quantum chemical data are extensively used in the study of the organic
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compounds reaction mechanisms. Table S1 presents the calculated zero-point vibrational energies, rotational constants, entropies and dipole moment by using B3LYP/6-31++G(d,p)
3.5.
AC C
level for the compound.
Electronic Properties
According to the molecular orbital theory; the atoms in the essential bond distance close to each other when the molecules occurring the molecule leading to the formation, s, p and d atomic orbitals mix and form orbitals belonging to the molecule. These orbitals could be considered as the places where the probability of electrons in the molecule is great [31]. The highest occupied molecular orbital energy (EHOMO) and the lowest unoccupied molecular 11
ACCEPTED MANUSCRIPT orbital energy (ELUMO) are the basis orbitals participated in the chemical reaction. The HOMO energy (πdonor) is the energy of a molecule giving an electron and the LUMO energy (πacceptor) is the energy of a molecule taking an electron [32]. The energy gap between the HOMOLUMO orbitals characterizes the electron conductivity and the spectroscopic properties of the molecules. An electronic system with a larger HOMO–LUMO gap should be less reactive
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than one having a smaller gap [33]. The HOMO-LUMO gap is high the charge transportation is not probable and the molecule is stable or non-reactive. In this study, HOMO and LUMO energies of the compound were listed in Table S2. The HOMO–LUMO gap values of the studied molecules were calculated between 5.08 and 5.06 eV in B3LYP/6-31++G(d,p) and
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B3LYP/6-311++G(d,p) levels as seen in Figure S1.
The Sum of electronic and zero-point energies of the compound was calculated between 1577.1096 (a.u.) for the compound 1 by using B3LYP/6-31++G(d,p) level. Also the chemical
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hardness (η) and the electron affinity (A) of the molecules can be calculated from the HOMOLUMO orbitals. The chemical hardness value of the compound 1 is 2.54 eV and 2.53 eV. The electron affinity (A), the electronegativity (χ) and the chemical softness (S) of the molecules were given in Table S2.
The ESP (Electrostatic Surface Potential) that associated with partial charge and
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electronegativity and MEP (Molecular Electrostatic Potential) plots exhibit the distribution of charge of compounds with respect to the difference between positive and negative charge [32]. The MEP map of the surface presented in molecular size also shows the shape and electrostatic potential value. The different colors in the MEP surfaces show different values of
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the electrostatic potentials. In the MEP map red regions show the negative potentials, rich electron regions and blue regions show the positive potentials poor electron regions [34]. The
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deepest blue defines strongest attraction and the deepest red describes strongest repulsion. In the MEP of the compound 1 potential change from -0.04323 a.u. to 0.04323 a.u. as seen from Figure S2.
For the compounds 1 the red-orange regions seen over the sulphur atom so the compound 1 shows nucleophilic reactivity property because of the electron density on the sulphur atoms. A density of states diagram of the molecular orbital of the compounds 1 is shown in Figure S3. This graph was drawn by Gausssum2.1 [35]. The NBO analysis reveal that the bond strength, proton affinity and position of O–C, CC, C-P, N-P groups have major influence on the reactivity of considered molecules [36]. 12
ACCEPTED MANUSCRIPT Table S3 shows the intramolecular, rehybridization and delocalization of electron density (ED) of the compound 1. Both compounds; in the σ (C7-C9) bond C7 bond hybrid of the C7C9 bond gains 36.01% and 35.95% in s character and 63.96% and 64.01% in p character (with hybrid orbital sp1.78 and sp1.78). For the compound 1, C6-C8 bond has σ bond C6 bond
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hybrid of the C6-C8 bond gains 38.11% in s character and 61.85% in p character.
4. Conclusion
Amidodithiophosphonates 1-3 were synthesized and characterized by elemental 13
C- and
31
P- NMR spectroscopy. The molecular structures of the
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analyses, IR, 1H-,
compound 1 have been studied by using the ab initio calculations method based on B3LYP.
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The experimental and theoretical calculations on vibrational frequencies, 1H-NMR and
13
C-
NMR spectra are very close to each other. Highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) of the compound 1 have been predicted. In addition, the thermodynamic parameters such as total thermal energy, entropy, heat capacity,
Acknowledgements
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thermal enthalpies and thermal free energies values of the molecules were calculated.
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This study was supported by Pamukkale University (Grant no: 2009FBE020 and
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2012BSP004). Computation has been performed using TUBITAK/ULAKBIM clusters.
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ACCEPTED MANUSCRIPT [3] A. Mesparo, I. Kani, A.A. Mohammed, M.A. Omary, J.P. Fackler, Jr, Syntheses and Structures of Dinuclear Gold(I) Dithiophosphonate Complexes and the Reaction of the Dithiophosphonate Complexes with Phosphines: Diverse Coordination Types, Inorg. Chem. 42 (2003) 5311-5319. [4] W.E. Van Zyl, R.J. Staples, Jr. J.P. Fackler, Dinuclear gold(I) dithiophosphonate complexes: formation, structure and reactivity, Inorg. Chem. Comm. 1 (1998) 51-54.
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[7] M.C. Aragoni, M. Arca, F. Demartin, F.A. Devillanova, C. Graiff, F. Isaia, V. Lippolis, A. Tiripicchio, G. Verani, Reactivity of phosphonodithioato Ni-II complexes: solution equilibria, solid state studies and theoretical calculations on the adduct formation with some pyridine derivatives, J. Chem. Soc. Dalton Trans. (2001) 2671-2677. [8] E.G. Saglam, A. Ebinç, C. T. Zeyrek, H. Unver, T. Hokelek, Structural studies on some dithiophosphonato complexes of Ni(II), Cd(II), Hg(II) and theoretical studies on a dithiophosphonato Ni(II) complex using density functional theory, J. Mol. Struct. 1099 (2015) 490-501.
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[11] G. Saglam, E. O. Celik, H. Yilmaz, N. Acar, Synthesis and Spectroscopic Characterization of Novel Aryldithiofluorophosphonate Derivatives and X-Ray Studies of [(4-CH3OC6H4)(F)P(S)S-][PH4P+], Phosphorus, Sulfur, Silicon and Relat. Elem. 187 (2012) 1339-1346. [12] M.D.C. Hernandez-Galindo, M. Moya-Cabrera, V. Jancik, R.A. Toscano, R. CeaOlivares, Synthesis and structural characterization of organotellurium(IV) complexes bearing ferrocenyldithiophosphonate ligands. The first examples of tellurium dithiophosphonates, J. Organomet. Chem. 280 (2014) 772-773. [13] M. Karakus, S. Solak, T. Hökelek, H. Dal, A. Bayrakdar, S. Özdemir Kart, M. Karabacak, H.H. Kart, Synthesis, crystal structure and ab initio/DFT calculations of a derivative of dithiophosphonates, Spectrochim. Acta Part A 122 (2014) 582–590. [14] H.H. Kart, S. Özdemir Kart, M. Karakus, M. Kurt, Ab initio/DFT calculations of tertbutyl ammonium salt of O,O'-dibornyl dithiophosphate, Spectrochim. Acta Part A 129 (2014) 421-428. 14
ACCEPTED MANUSCRIPT [15] M.A. Palafox, G. Tardajos, A.G. Martines, V.K. Rastogi, D. Mishra, S.P. Ojha, W. Kiefer, FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular geometry of biomolecule 5-aminouracil, Chem. Phys. 340 (2007) 17–31. [16] M. Karabacak, E. Sahin, M. Cinar, I. Erol, M. Kurt, X-Ray, FT-Raman, FT-IR spectra and ab initio HF, DFT calculations of 2-[(5-methylisoxazol-3-yl) amino]-2- oxo-ethyl methacrylate, J. Mol. Struct. 886 (2008) 148-157.
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[17] F. Ucun, V. Guclu, A. Saglam, Ab initio Hartree-Fock and density functional theory study on molecular structures, energies, and vibrational frequencies of conformations of 2-hydroxy-3-nitropyridine and 3-hydroxy-2-nitropyridine, A. Spectrochim. Acta A 70 (2008) 524-531.
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[18] M. Karabacak, A. Coruh, M. Kurt, FT-IR, FT-Raman, NMR spectra, and molecular structure investigation of 2,3 Dibromo-N-Methylmaleimide: A combined experimental and theoretical study, J. Mol. Struct. 892 (2008) 125–131. [19] C. Lee, W. Yang, R.G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B37 (1988) 785-789.
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[20] M. Kaupp, M. Bühl, V.G. Malkin, Calculation of NMR and EPR parameters: theory and applications; Wiley-VCH: Weinheim, 2004. [21] A. Bayrakdar, H.H. Kart, S. Elcin, H. Deligoz, M. Karabacak, Synthesis and DFT calculation of a novel 5,17-di(2-antracenylazo)-25,27-di(ethoxycarbonylmethoxy)26,28-dihydroxycalix[4]arene, Spectrochim. Acta Part A 136 (2015) 607-617.
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[22] J. Casanovas, A.M. Namba, S. Leon, G.L.B. Aquino, D.V.J. da Silva, C. Aleman, Calculated and experimental NMR chemical shifts of p-menthane-3,9-diols. A combination of molecular dynamics and quantum mechanics to determine the structure and the solvent effects, J. Org. Chem. 66 (2001) 3775-3782.
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[23] V.G. Albano, M.C. Aragoni, M. Arca, C. Castellari, F. Demartin, F. Isaia, V. Lippolis, L. Loddo, G. Verani, An unprecedented example of a cis-phosphonodithioato nickel(II) complex built by an extensive hydrogen bonding supramolecular network, Chem. Commun. (2002) 1170-1171.
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[24] M. Karakus, Synthesis and Characterization of Chiral Gold(I) Phosphine Complexes with New Dithiophosphorus Ligands, Phosphorus, Sulfur Silicon Relat. Elem. 186 (2011) 1523-1530. [25] J. B. Foresman A. E. Frisch (1996) Exploring Chemistry with Electronic Structure Methods, Gaussian Inc. [26] Gaussian 09, Revision C.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, 15
ACCEPTED MANUSCRIPT A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2010. [27] R. Dennington, T. Keith, J. Millam, GaussView, Version 5; Semichem Inc., Shawnee Mission, KS, 2009.
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[28] J. Tomasi, B. Mennucci, R. Cammi, Chem. Rev. 2005, 105, 2999-3093. [29] Davut Avcı Æ Yusuf Atalay, Effects of different GIAO and CSGT models and basis sets on 2-aryl-1,3,4-oxadiazole derivatives,Struct Chem (2009) 20:185–201
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[30] S. Karpagam, R. Thangaraj, S. Guhanathan, Functional modification of poly(vinyl alcohol) through phosphorus containing nitrogen heterocyclic moieties, J Appl. Polym. Sci. 110 (2008) 2549-2554.
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[31] D. Avcı, The Investigation of Spectroscopic and Optical Properties of Some Aromatic Molecules Including Heteratom, Sakarya University Institute of Science, PhD. Thesis 2009. [32] N. Günay, H. Pir, Y. Atalay, Theoretical investigation of spectroscopic properties of lasparaginium picrate molecule, SAU Sci and Lit J 2011, 1, 15. [33] R. Kurtaran, S. Odabasoglu, A. Azizoglu, H. Kara, O. Atakol, Experimental and computational study on [2,6-bis(3,5-dimethyl-N-pyrazolyl)pyridine](dithiocyanato)mercury(II), Polyhedron 26 (2007) 5069-5074.
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[34] N. Dege, N. Senyuz, H. Batı, N. Gunay, D. Avcı, O. Tamer, Y. Atalay, The synthesis, characterization and theoretical study on nicotinic acid [1-(2,3dihydroxyphenyl)methylidene]hydrazide, Spectrochim. Acta Part A 120 (2014) 323-331.
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[35] N. M. O'Boyle, A. L. Tenderholt, K. M. Langner, Cclib: a library for package‐independent computational chemistry algorithms, J. Comp. Chem. 29(5) (2008) 839-845.
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[36] M. T. Tari, N. Ahmadinejad, Theoretical N-14 and O-17 nuclear quadrupole resonance parameters for tirapazamine and related metabolites, Struct. Chem. 25, (2014) 1281-1287.
16
ACCEPTED MANUSCRIPT Table Captions Table 1. Theoretical NMR calculations for the compound 1. Table 2. Vibrational wavenumbers of the compound 1 obtained from B3LYP/6-31++G(d,p) in cm-1, experimental frequencies from FT-IR Spectra (4000 to 450 cm-1), IR
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Intensities (km mol-1), and assignment with TED percentage in square brackets. Table S1. Calculated thermodynamic parameters of the compound 1. Table S2. Electronic parameters of the compound 1.
Table S3. The hybrids of selected natural bond orbitals calculated by NBO analysis for the
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compound 1 by using B3LYP/6-31++G(d,p) level.
Table 1. Theoretical NMR calculations for the compound 1. Atom number Exp. 6-C 159.06
Gas phase 6-31++ G(d,p) 159.64
DMSO
6-311++ G(d,p) 170.8109
17
6-31++G(d,p) 160.69
6-311++ G(d,p) 171.97
ACCEPTED MANUSCRIPT
12-H 4-H 3-H 2-H 33-H 32-H 48-H 39-H 34-H 28-H 21-H 31-H 36-H 30-H 26-H 46-H 42-H 35-H 45-H 47-H 43-H 38-H 41-H
6.82 6.82 3.76 3.76 3.76 2.91 1.5 1.8 1.8 1.7 2.91 1.36 2.25 2.25 1.86 1.06 1.06
140.90 138.20 133.84 124.00 115.30 57.42 52.86
46.90 46.70 46.27 45.97 37.65 30.17
47.3675 48.4767 47.0063 45.9688 37.242 31.6523
46.90 46.52 46.14 46.14 37.15 30.00
48.26 47.33 46.85 46.10 36.71 31.48
28.94 24.79 24.15 8.36 7.88 7.15
29.8268 25.2687 24.4298 8.4364 7.8579 7.159
28.52 24.30 23.78 8.37 7.95 7.28
6.92 4.16 3.77 3.74 3.19 2.63
6.8549 4.0703 3.6744 3.6744 3.1776 2.7166
7.27 4.27 3.93 3.93 3.20 2.88
7.19 4.19 3.87 3.84 3.19 2.96
2.7154 2.4945 2.441 2.2296 2.1471 1.8779
2.87 2.53 2.43 2.33 2.20 2.02
2.95 2.50 2.51 2.28 2.21 1.88
2.01 1.92 1.80 1.70 1.41 1.21
1.991 1.9173 1.7496 1.66 1.3759 1.2008
2.02 1.94 1.85 1.70 1.44 1.25
2.00 1.93 1.80 1.67 1.40 1.25
1.08 0.99 0.99 0.86 0.81
1.158 1.1342 1.0109 0.9566 0.8521
1.08 1.00 0.98 0.88 0.80
1.15 1.13 1.01 0.98 0.84
2.60 2.53 2.36 2.28 2.14 2.01
1.86 1.06 0.78 0.78 1.8 0.78
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130.59 127.04 125.64 115.48 107.24 54.71 50.96
29.37 24.78 24.02 8.45 7.93 7.28
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27.49 18.8 18.8 32.23 7.91 7.91
140.8236 138.2808 135.2097 123.747 113.1921 56.7122 52.8887
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44-C 40-C 23-C 15-H 14-H 10-H
44.21 38.76 42.45 40.46 22.76 25.33
130.56 127.15 126.92 115.20 105.36 53.97 50.97
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29-C 22-C 24-C 27-C 37-C 25-C
130.51 130.51 140.88 111.81 111.81 55.02
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9-C 13-C 7-C 8-C 1-C 20-C
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11-C
Table 2. Vibrational wavenumbers of the compound 1 obtained from B3LYP/6-31++G(d,p) in cm-1, experimental frequencies from FT-IR Spectra (4000 to 450 cm-1), IR Intensities (km mol-1), and assignment with TED percentage in square brackets.
18
ACCEPTED MANUSCRIPT Mode no.
Ir Exp 5.09
Unscaled
Scaled
Assignment [TED]≥10% a
317
ʋSP(38)
27
393
377
δCPN(16)
30
0.01
423
406
τHCCCring(79)
32
38.37
455
437
ʋPC(13) + ʋSP(10)
33
23.68
509
489
δCOC(15)
34
25.19
511
491
ʋPS
35
18.58
532
511
τHCOC(42) + ωCHring
38
25.82
617
592
ʋasymPS
644
618
δCCCring
678
651
δHSP(12) + ʋasymPS
731
702
τHCCCring(57)
817
784
ʋCC(37) + τHCCC(13) + ʋPN
831
798
δHSP(13) + τHCCC(23)
555 PS2 sym 555 PS2 sym 644 PS2 asym
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330
1.3
23
4.25
42
93.33
43
2.12
47
25.37
49
20.15
50
15.84
826 PN
849
815
τHCCO(30) + ʋPN + ωCHring
51
59.01
826 PN
852
818
τHCCO(13) + ʋPN + ωCHring
52
3.16
53
29.49
55
2.72
56
2.27
57
2.12
58
0.89
60
0.92
61
7.17
62
0.94
63
0.76
65
4.17
66
49.78
67
118.3
69
17.17
70
121.1
71
0.21
826 PN
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644 PS2 asym
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40
876
841
ʋCC(19)
884
849
ʋPN + ρHCC
932
895
ʋCC(33)
952
914
ʋCC(15)
966
927
δHCC(13)
969
930
τHCCC(10) + τHCCH(67)
990
950
τHCCH(12) + τHCCO(18)
1006
966
δHCC(18)
1019
978
δHCC(26)
1023
982
δCCC + δHCC
1051
1009
ʋCC(29)
1253 CO
1060
1018
ʋCC(10) + ʋOC(73)
1105 CN
1086
1043
ʋNC(64)
1118
1073
ʋCC(18)
1119
1074
ʋCC(12) + ʋPC(19)
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826 PN
1092
ʋCC(15)
1140
1094
δHCHring(15) + ʋCCring(21)
12.93
1171
1124
δHCH(83) + ʋCC(14)
7.47
1205
1157
δHCH(30) + δHCO(10)
60.95
1208
1160
δHCO(60) + ʋCCring(12)
0.69
1212
1164
δHCC(46)
79
0.35
1225
1176
δHCC(28)
80
1.28
1232
1183
ʋCC(11)
81
8.15
1245
1195
δHCN(30)
83
20.28
1271
1220
δHCN(42)
84
288.5
1294
1242
ʋCCring(51) + ʋCOring + δHCCring
85
2.94
1296
1244
δHCC(33)
87
1.51
1319
1266
δHCC(50)
72 74 76 77 78
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1137
5.83
1253 CO
19
ACCEPTED MANUSCRIPT 15.55
1329
1276
δHCCring(65)
89
5.02
1344
1290
δHCC(31) + τCH2
90
1348
1294
ʋCCring(56)
91
47.4 1467 C=C aromatic 2.21
1361
1307
δHCC(33) + τCH2
92
3.48
1380
1325
δρHCC(29)
93
1.73
1381
1326
δHCH(10)
94
3.82
1401
1345
δHNP(33)
95
5.96
1409
1353
δHCC(34)
96
9.5
1429
1372
δHCH(56) + ωCH3
97
68.21
1435
1378
δCNH(48)
98
18.66 1467 C=C aromatic 12.69
1445
1387
δHCHring(26) + ʋCCring
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88
1421
δHCH(71)
2.17
1490
1430
δHCH(72)
101
2.29
1491
1431
δHCH(69)
102
0.24
1498
1438
δHCH(70)
103
8.72
1499
1439
δHCH(98)
104
11.94
1506
1446
δHCH(63)
105
43.44
1508
1448
δHCH(69)
106
5.82
1513
1452
δHCH(64)
107
11.31
1520
1459
δHCH(64)
108
10.48
1521
1460
δHCH(59)
109
5.09
1529
1468
δHCH(74)
110
90.85
1536
1475
δHCH(38) + ʋCCring
111
28.48 1594 C=C aromatic 172.4 1594 C=C aromatic
1608
1544
δHCCring(11) + ʋCCring(68)+ δCNH
1645
1579
ʋCCring(61) + δHCCring
2701
2593
ʋSH(100)
3017
2896
ʋCH(90)
3024
2903
ʋsymCH3(91)
3028
2907
ʋsymCH3(88)
3030
2909
ʋCH(87)
3033
2912
ʋsymCH(89)
112
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99
SC
1480
100
113
1.24
114
9.51
115
62.73
116
14.97
117
25.78
118
44.61
119
76.86
3038
2916
ʋCH(91)
120
22.87
3043
2921
ʋCH(86)
121
81.54
3049
2927
ʋCH(86)
122
40.26
3052
2930
ʋCH(87)
123
37.74
3060
2938
ʋCH(77)
124
16.02
3063
2940
ʋCH(82)
125
9.9
3082
2959
ʋasymCH3(91)
127
82.06
3088
2964
ʋasymCH2(82)
128
26.8
3090
2966
ʋasymCH3(94)
130
23.21
3118
2993
ʋCH(85)
131
44.5
3133
3008
ʋCH(88)
132
26.46
3148
3022
ʋasymCH3(91)
133
20.22
3158
3032
ʋCH(91)
AC C
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2911 C-H alipatic
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ACCEPTED MANUSCRIPT 134
1.33
3205
3077
ʋasymCHring(92)
135
0.19
3207
3079
ʋCH(93)
136
5.35
3219
3090
ʋCH(98)
137
8.96
3228
3099
ʋCH(98)
2983 C-H aromatic
32.06
3294 N-H 3573 3430 ʋNH(100 a TED: Total Energy Distribution, ʋ; stretching, δ; in-plane-bending, τ; torsion, ρ; rocking, ω; wagging, sym; 138
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symmetric, asym; asymmetric.
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ACCEPTED MANUSCRIPT HIGHLIGHTS
1. New amidodithiophosphonates were synthesized. 2. All compounds were characterized by IR,NMR(H-, 13C and 31P) spectroscopic
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methods. 3. IR, 1H NMR and 13C NMR of the compound 1 were computed using B3LYP method.
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4. The HOMO, LUMO energy gap of the compound 1 were theoretically calculated.