Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 130 (2014) 188–197

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Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion R. Singh, R.A. Yadav ⇑ Lasers and Spectroscopy Laboratory, Department of Physics, Banaras Hindu University, Varanasi 221005, India

h i g h l i g h t s

g r a p h i c a l a b s t r a c t

 Vibrational analysis of the

Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU) using the Gaussian-03 software. The experimental IR and the Raman spectra of the DTU molecule are given in the Figs. a and b respectively.

experimental IR and Raman spectra of DTU has been made.  Changes in vibrational characteristics of DTU are noticed due to radicalizations.  CAH out-of-plane bending frequency decreases in the DTU as compared to the others.

a r t i c l e

i n f o

Article history: Received 17 December 2013 Received in revised form 20 February 2014 Accepted 23 February 2014 Available online 12 March 2014 Keywords: FTIR and Raman spectra DFT studies Optimized molecular geometries GAPT charges Vibrational characteristics 2,4-Dithiouracil and its cation and anion

a b s t r a c t Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5AC6 bond length increases and loses its double bond character while the C4AC5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled NAH stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled. Ó 2014 Elsevier B.V. All rights reserved.

⇑ Corresponding author. Tel.: +91 542 2368593; fax: +91 542 2368390. E-mail addresses: [email protected], [email protected] (R.A. Yadav). http://dx.doi.org/10.1016/j.saa.2014.02.161 1386-1425/Ó 2014 Elsevier B.V. All rights reserved.

R. Singh, R.A. Yadav / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 130 (2014) 188–197

Introduction The nucleic acid bases with the sulfur atom(s) in place of the oxygen atom(s) have been a subject of different investigations as they have been detected in natural tRNA [1]. The sulfur atoms may induce considerable changes in the physicochemical properties of the bases and their interactions and further influence the structure of DNA bases. Although they have the same distributions of hydrogen acceptors and donors as the standard bases, the sulfur atom has larger radius and smaller electronegativity as compared to the oxygen atom. Hence, the thio-bases may have different physicochemical properties from the natural bases. Numerous sulfur-substituted bases have been used as drugs and hence these are important organic molecules from the pharmaceutical point of view. The derivatives of thio-uracil (TU) exhibit pharmacological activities [2,3]. 2,4-Dithiouracil (DTU) analogue were tested for anti-conflict and anaesthetic activity in rats and mice [4]. DTU molecule was found to be a melanoma-seeking agent owing to its specific incorporation in nascent melanin [5]. Thio-uracils are also used as marine corrosion inhibitors for steel [6,7] and as dental adhesives in the treatment of the metal surfaces [8]. In biological systems, the charge transfer is not only one of the most important means of interaction, but also one of the leading pathways of energy transfer. Vibrational spectra of thio-derivatives of cytosine, guanine and uracil have been investigated experimentally in our laboratory in the past [9–11]. Molecular geometries, charge distributions and vibrational characteristics of uracil (U), 2-TU, 4-TU and their radical cations have been investigated in details by our group [12]. The crystal structure of DTU has been determined by Schefter and Moutner using X-ray diffraction method [13]. Rostkowska et al. [14] reported the experimental IR spectra of 2-TU and 4-TU together with their N1 and N3 methylated derivatives isolated in low temperature inert matrixes. Comparisons of experimental IR absorption spectra of TUs isolated in low temperature Ar matrices have been made with ab initio and DFT calculations by Lapinski et al. [15]. Wo´jcik et al. [16] have recorded the experimental far IR and low frequency Raman spectra of polycrystalline DTU in the range of 50–400 cm1. Many workers have also studied the characteristics of tautomers of TUs, energies and uracil tetrade [17–20]. Kryachko et al. [21] have investigated influence of the protonation and deprotonation of TUs on their interaction with a single water molecule. The objective of the present work is to make the complete analysis of IR and Raman spectra of DTU in light of the results obtained from the DFT calculations at the B3LYP/6-311++g** level. Furthermore, the objective of the present work is also to notice the changes in the optimized molecular geometries, GAPT charges and vibrational characteristics of the DTU molecule as a result of cationic and anionic radicalizations.

Experimental DTU forms a yellow solid compound at ambient temperature. It was purchased from the Sigma–Aldrich Chemical Co. (USA) and was used as such without any further purification to record FT-IR and laser Raman spectra. The Perkin Elmer RX-1 spectrometer was used to record the IR spectrum and the Varian-3100 FTIR spectrometer was used for the far IR spectral study. The lead sulfide (PbS) is used as the IR detector in the FTIR spectrometer. The IR spectra of 2,4-DTU have been recorded in KBr pellet in the spectral range 400–4000 cm1 with the parameters: scans – 200, resolution – 4 cm1 and gain – 50. The far-IR spectrum of DTU has been recorded in Nujol mull in the spectral range 50–400 cm1.

189

The Raman spectrum was recorded using double monochromator and the Renishaw Raman spectrometer equipped with air cooled CCD and OLYMPUS microscope. The line 514.5 nm of an Ar+ laser was used for excitation of the sample and the spectrum was recorded in the region 50–3500 cm1. The following parameters were used to record the spectra: laser spot size – 1 lm, resolution 1 cm1, power at the sample <10 mW, integration time – 10 s, accumulation – 5, time constant – 10 s, one window covers 800 cm1, accuracy of measurements – 1 cm1, slit width fixed at the entrance of laser – 1 cm1. Computational details The computations were carried out to determine the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU) using the Gaussian-03 software [22]. The charges are described as corrected Mulliken charges through an overlap contribution which can be obtained on the basis of suitable terms derived from the computed APTs. On the other hand, Cioslowski proposed a straightforward definition of atomic charges based on APT invariants [23]. These charges, named generalized atomic polar tensor (GAPT) charges, can be immediately calculated by standard quantum chemical codes and these satisfy the requirement of neutrality of the molecule and are directly related to experimentally measurable quantities (i.e. IR intensities). These features contributed to the success of GAPT charges as a model alternative to the most used and popular schemes. The earlier articles have been more help to understand APT and GAPT charges. [24–26]. In order to obtain the reasonable frequency matching, scale factors proposed by Rauhut and Pulay [27] were employed. The initial geometrical parameters were taken from the previous work [12] and calculations were performed using the B3LYP method and employing the 6-311++G** basis set. For the radical cation and anion, calculations were also performed at the B3LYP/ 6-311++G** basis set with the unrestricted approach. The geometries were optimized by minimizing the energies with respect to all the geometrical parameters without imposing any molecular symmetry constraints. The assignments of the normal modes of vibration for all the three molecules have been made by visual inspection of the individual mode using the Gauss View software [28]. Results and discussion Molecular structure The labeling scheme for the studied molecules is shown in Fig. 1. The optimized geometrical parameters for the DTU molecule and its radical cation and anion calculated at the B3LYP/6-311++G** level alongwith the experimental parameters for the DTU molecule are collected in Table 1. The present calculations predict that the neutral molecule as well as its both the radicals possess planar structures with Cs point group symmetry. The GAPT charges at atomic sites of the three molecules are collected in Table 2 and also shown in Fig. 2. Neutral molecule The presently calculated NAC bond lengths are found in the range 1.374–1.394 Å, with the reported experimental range 1.342–1.406 Å [13]. The atomic charge on the C2 atom is found to be more than that on the C4 atom and thus, the C2 atom pulls

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(a) DTU

(b) DTU

(c) DTU

+

-

Fig. 1. Labeling scheme for the (a) DTU, (b) DTU+ and (c) DTU molecules.

the N3 atom more strongly towards itself as compared to the C4 atom which results in the shortening of the C2AN3 bond as compared to the C4AN3 bond. Sulfur atom is more electronegative than the hydrogen atom and thus, the S8 atom pulls the C2 atom towards itself which results in the lengthening of the C2AN1 bond as compared to N1AC6. The present calculation predicts the C5@C6 bond length to be 1.351 Å where as C4AC5 is calculated to be 1.441 Å. The N atom is more electronegative than the C atom and the C2 atom is surrounded by two N atoms (N1 and N3) where as C4 is surrounded by one C atom (C5) and one N atom (N3) atom. Thus, N3 and N1 together pull more charge from the C2 atom as compared to the charge that N3 and C5 together pull from the C4 atom as a result of which the C2AS8 bond length is slightly (0.002 Å) greater than the C4AS10 bond length. The atomic charge on the C5 atom is found to be negative while that on the C6 is positive, suggesting that the C5AH11 bond length is shorter than the C6AH12 bond length. The magnitude of the bond angle C2AN3AC4 is greater than C2AN1AC6 by 4.40° which could be due to the two S atoms near the N3 atom. The bond angle C5AC4AN3 is calculated to be shorter than N1AC6AC5 by 7.21° because of the presence of the S atom at the C4 site. The S atom at the C2 site pulls the N1AH7 bond towards

itself due to its electronegative character resulting in shortening of the bond angle C2AN1AH7 by 5.58° as compared to the bond angle C6AN1AH7. Similarly, the bond angle C4AC5AH11 is shorter than the bond angle C6AC5AH11 by 2.60° due to presence of the S10 atom at the C4 site. The N3 atom in the ring pulls the S10 atom towards itself resulting in the shortening of the bond angle N3AC4AS10 with respect to C5AC4AS10 by 4.53°. Similarly, the bond angle N1AC6AH12 is calculated to be shorter than the bond angle C5AC6AH12 by 8.54°. Radical cations In DTU+ the bond lengths N1AC6 and N3AC4 are found to decrease as compared to the neutral DTU molecule because the atomic charges on the N atoms increase whereas those on all the C atoms (except on the C5 atom) decrease. The N1AC2 bond length is found to be unaffected. As the atomic charge on the S8 atom becomes positive (Table 2 and Fig. 2) the S8 atom pulls the C2 atom less strongly towards itself as compared to the neutral molecule which results in the lengthening of the C2AN3 bond in DTU+. Removal of an electron from the neutral DTU molecule induces the negative charge on the C4 atom, which pulls the C5 atom towards itself more strongly and results in the shortening of the

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191

Table 1 Optimized geometrical parametersa of DTU, DTU+ and DTU. Definition

(N1AC6) (N1AC2) (N1AH7) (C6AH12) (C6AC5) (C5AH11) (C5AC4) (C4AN3) (C4AS10) (N3AH9) (N3AC2) (C2AS8) a (C6AN1AC2) a (C6AN1AH7) a (C2AN1AH7) a (N1AC6AH12) a (N1AC6AC5) a (H12AC6AC5) a (C6AC5AH11) a (C6AC5AC4) a (H11AC5AC4) a (C5AC4AN3) a (C5AC4AS10) a (N3AC4AS10) a (C4AN3AH9) a (C4AN3AC2) a (H9AN3AC2) a (N1AC2AN3) a (N1AC2AS8) a (N3AC2AS8)

r r r r r r r r r r r r

a b

DTU b

DTU+

DTU

Cal

Exp

Cal

Cal

1.37 1.38 1.01 1.08 1.35 1.08 1.44 1.39 1.66 1.01 1.37 1.66 123.6 121.0 115.4 115.6 121.2 123.2 121.4 119.9 118.8 114.0 125.3 120.7 116.5 128.0 115.6 113.3 122.8 123.9

1.36 1.34 0.59 1.04 1.37 0.92 1.41 1.36 1.69 0.95 1.41 1.65 126.6 117.0 113.0 123.0 119.2 117.0 123.0 118.9 118.0 117.4 123.2 119.3 76.0 125.5 155.0 112.4 125.9 121.7

1.36 1.38 1.01 1.08 1.36 1.08 1.42 1.37 1.69 1.02 1.40 1.65 124.2 119.8 116.0 116.1 121.4 122.6 120.9 118.3 120.7 117.1 123.4 119.5 119.3 126.0 114.7 113.0 124.6 122.4

1.42 1.35 1.01 1.08 1.39 1.08 1.39 1.45 1.72 1.01 1.35 1.71 123.9 121.0 115.1 116.3 117.8 125.9 119.6 122.1 118.3 114.3 129.1 116.6 116.3 126.3 117.4 115.6 121.4 123.0

Fig. 2. APT Charges at different atomic sites in DTU, DTU+ and DTU.

Bond lengths (r) in Å and angles (a) in degrees. Ref. [17].

Table 2 APT atomic charges for DTU, DTU+ and DTU. Atom

DTU

DTU+

DTU

N1 C2 N3 C4 C5 C6 H7 S8 H9 S10 H11 H12

0.75 1.12 0.84 0.97 0.46 0.57 0.25 0.62 0.20 0.58 0.09 0.06

0.03 0.29 0.52 0.36 0.01 0.07 0.24 0.20 0.05 0.43 0.13 0.16

0.49 0.91 0.71 0.75 0.02 0.19 0.20 0.80 0.19 0.90 0.04 0.02

C4AC5 bond length. In the DTU cation, the atomic charge on the C5 atom becomes less negative and the C6 atom acquires the negative charge causing repulsion between them which increases the C5@C6 bond length. The C2@S8 bond length decreases by 0.014 Å while the bond length C4@S10 increases by 0.035 Å due to removal of an electron from the neutral DTU molecule. The bond lengths of the two NAH bonds are found to increase slightly as the atomic charges are calculated to increase due to removal of an electron (Fig. 3). The magnitude of the angle C2AN3AC4 shortening by 2.0° in going from DTU to DTU+. Since the atomic charge on the S10 atom becomes more positive as compared to the atomic charge on S8 atom in DTU+, S10 repels the H9 atom more strongly as compared to the S8 atom which results in increase of the bond angle C4AN3AH9 by 2.2° while the bond angle C2AN3AH9 shortening by 1.1° as compared to that in the DTU molecule. It can be seen from the Table 2 that in DTU+ the atomic charge on the C5 atom is negative while the atomic charge on the S10 atom is positive

Fig. 3. Variation of N1/3AH7/9 and C2/5AS8/10 bond lengths in DTU, DTU+ and DTU–.

and thus, the C5 and S10 atoms attract towards each other resulting in shortening of the bond angle S10AC4AC5 by 1.9° as compared to that in the DTU molecule. The magnitude of the bond angle H11AC5AC4 increases by 1.9° in going from DTU to DTU+ ion because of the positive charge on the S10 atom in the DTU+ ion due to which it repels the H11 atom. Removal of an electron in the DTU molecule induces negative charge on the C6 atom (Table 2 and Fig. 2) as a result of which it pulls the H7 atom towards itself resulting in shortening of the bond angle C6AN1AH7. The magnitude of the bond angle N1AC2AS8 increases by 1.8° while the magnitude of the bond angle N3AC2AS8 shortening by 1.5° in going from the neutral DTU molecule to the DTU+ ion. Radical anion Due to addition of an electron to the neutral DTU molecule the lengths of the N1AC6 and N3AC4 bonds increase while the bond lengths N1AC2 and N3AC2 decrease. As a result of anionic radicalization, the C5AC6 bond length increases by 0.043 Å and loses its double bond character while the C4AC5 bond length decreases by 0.051 Å. It can be seen from the Table 2 that the atomic charges

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on both the S atoms decrease in going from the neutral to the anionic species as a result of which both the C@S bond lengths are found to increase (Fig. 3). Similarly, the atomic charges on both the N atoms are found to increase in going from the neutral DTU molecule to its radical anion resulting in shortening of both the NAH bond lengths (Table 1 and Fig. 3). It is found that the C6AH12 bond length decreases while the C5AH11 bond length increases in going from the neutral DTU molecule to the DTU ion. Out of the two CANAC angles, the angle C2AN3AC4 shortening by 1.7° while the angle C6AN1AC2, remains practically unaffected as a result of anionic radicalization. Similarly, in going from the DTU molecule to its radical anion one of the two NACAC angles, namely, N1AC6AC5, shortening by 3.4° while the angle N3AC4AC5 dose not change. It can be seen from the Table 2 that the atomic charge on the H11 atom decreases in going from the DTU molecule to the DTU radical and thus, in the DTU ion the H11 atom pulls the C5 atom towards itself less strongly as compared to that in neutral DTU, which results in increment of the C4AC5AC6 angle by 2.2°. Similar case is found for the NACAN bond angle. It can be seen that the atomic charge on the S10 atom is more negative and therefore, it pulls the atomic charge from the N3 atom resulting in decrement of the N3AC4AS10 angle by 4.1° which further results in increment of the angle C5AC4AS10. It is noticed that the atomic charge at the C6 site decreases resulting in increment in the bond angles N1AC6AH12 and C5AC6AH12 by 0.7° and 2.6°, respectively. As a result of anionic radicalization the magnitude of the bond angle C6AC5AH11 shortening by 1.7° whereas the magnitude of the bond angle C2AN3AH9 increases by 1.8°. Vibrational analysis The experimental IR and Raman spectra are shown in Figs. 4 and 5 respectively neutral DTU molecule. The computed IR and Raman spectra for all the three molecules are compared in Figs. 6 and 7 respectively. The fundamental frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the DTU molecule and its cationic and anionic radicals computed at the B3LYP/6-311++G** level are

collected in Table 3. As mentioned earlier each of the studied molecules possesses planar structure with Cs point group symmetry. Each molecule, being twelve atomic, has 30 normal modes of vibration which are distributed between the two species a0 and a00 as: 21 a0 + 9 a00 . The modes under both the species a0 and a00 are Raman as well as IR active. Moreover, the a0 modes are expected to be polarized and the a00 modes as depolarized in the Raman spectrum. Neutral molecule Ring modes. The six ring stretching modes (m26, m24, m22, m21, m18 and m11) Table 3 involve stretching of the four CAN and two CAC bonds. The highest ring stretching mode frequency (m26) is calculated to be 1651 cm1 with strong IR intensity and Raman activity and is identified easily as the C@C stretching mode. The corresponding IR and Raman bands have been observed at 1613 and 1608 cm1 with strong intensities. The ring stretching mode m24 have also been strongly observed at 1484 and 1495 cm1 in the IR and Raman spectra, respectively, and the corresponding calculated frequency is found to be 1492 cm1 (Table 3) with strong IR intensity and low Raman activity. The calculated frequency corresponding to this mode (m22) is 1362 cm1 with medium strong IR intensity and weak Raman activity. The ring stretching mode (m21) is calculated to be 1257 cm1 with very weak IR intensity. The corresponding observed frequencies have very strong IR and Raman intensities. The ring stretching mode (m18) has been calculated to be 1125 cm1 with very high IR intensity and very weak Raman activity. The observed frequencies 1133 and 1125 cm1 for this mode appear with very strong intensities in the IR and Raman spectra respectively. The frequencies 695 cm1 with medium strong intensity in the IR spectrum and 691 cm1 with very strong intensity in the Raman spectrum have been assigned to the ring stretching mode (m11) corresponding to the ring breathing mode and the calculated frequency for this mode has been found to be 694 cm1 with weak IR intensity and Raman activity. All the six ring stretching modes of DTU agree with those of U, 2-TU and 4-TU [12]. One (m16) of the three ring angle bending modes (m16, m7 and m6) has been observed at 984 cm1 with strong intensity in the IR

Fig. 4. Experimental IR spectra of DTU.

R. Singh, R.A. Yadav / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 130 (2014) 188–197

193

Fig. 5. Experimental Raman spectra of DTU.

Fig. 7. Calculated Raman spectra of DTU and its ionic radicals.

[12] reported the observed frequencies for the three ring in-plane bending modes for U, 2-TU and 4-TU in the range 430–600 and 970–1000 cm1. The frequency corresponding to the ring out-of-plane bending mode m4 has been observed strongly at 377 cm1 in the Raman spectrum only and its magnitude is calculated to be 383 cm1 with weak IR and Raman bands. The frequencies for the remaining two out-of-plane bending modes (m1 and m2) have not been observed due to their lower magnitudes which lie beyond the experimentally investigated region of the IR and Raman spectra. From the calculations, these two modes have been assigned at 116 and 138 cm1 with very weak IR intensities and Raman activities. The ring out-of-plane bending mode for U, 4-TU and 2-TU were reported in region 100–400 cm1 by Singh et al. [16].

Fig. 6. Calculated IR spectra of DTU and its ionic radicals.

spectrum only and it is calculated to be 987 cm1 with very weak IR intensity and Raman activity with lower magnitude of depolarization ratio. The observed frequencies 447 and 453 cm1 appear strongly in the IR and Raman spectra and are assigned to the second ring in-plane bending mode (m7). The calculated vibrational frequency for the mode (m7) has been found to be 464 cm1 with the weak IR intensity and Raman activity. The third ring in-plane bending mode (m6) is calculated to have frequency 445 cm1 with weak intensity in the IR spectrum and low Raman activity. The Raman spectrum it is weakly observed at 424 cm1. Singh et al.

CAH modes. The two CAH stretching modes (m28 and m27) are found to be pure modes and are highly localized modes. In the present study, the two CAH stretching modes are calculated to be 3249 and 3212 cm1 with weak IR intensities, strong Raman activities and polarized Raman bands. The bands observed in the FTIR spectrum at 2896 and 2930 cm1 are assigned to the two CAH stretching vibrations. Yadav et al. [9] observed the two CAH stretching frequencies for 2-TU at 3136 and 3200 cm1. The two CAH in-plane bending modes (m19 and m17) appear as sharp bands but with strong and weak medium intensities. The calculated frequencies 1213 and 1082 cm1 are assigned to the CAH in-plane bending vibrations with the corresponding IR bands at 1211 and 1076 cm1 and the Raman bands at 1195 and 1080 cm1 respectively. These two CAH in-plane bending modes are assigned in the range 1060–1217 cm1 by Singh et al. [12] for U, 2-TU and 4TU molecules. The bands corresponding to the two out-of-plane CAH deformation modes (m15 and m13) for the DTU molecule are calculated to be 959 and 792 cm1. The observed frequency 795 cm1 could be correlated to the lower CH out-of-plane bending mode (m13). For U, 4-TU and 2-TU molecules these two CAH out-of-plane bending modes have been reported in the range 800–970 cm1 by Singh et al. [12].

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Table 3 Calculated and observed fundamental frequenciesa (cm1) of DTU, DTU+ and DTU. S. No.

DTU Cal

m1 m2 m3 m4 m5 m6 m7 m8 m9 m10 m11 m12 m13 m14 m15 m16 m17 m18 m19 m20 m21 m22 m23 m24 m25 m26 m27 m28 m29 m30

Obs

Unscaled

Scaled*

116 (0.2, 0.02) 0.75 138 (0.04, 0.02) 0.75 215 (5, 8) 0.68 383 (16, 0.5) 0.75 388 (0.04, 2) 0.57 445 (8, 20) 0.17 464 (16, 10) 0.32 578 (31, 2) 0.75 612 (13, 3) 0.75 665 (0.13, 0.4) 0.75 694 (1, 24) 0.06 707 (73, 1) 0.75 792 (29, 0.02) 0.75 879 (14, 1) 0.72 959 (0.0, 2) 0.75 987 (20, 2) 0.18 1082 (25, 15) 0.22 1125 (360, 20) 0.61 1213 (166,18) 0.33 1240 (55, 36) 0.08 1257 (36, 68) 0.55 1362 (36, 21) 0.17 1397 (9, 21) 0.43 1492 (64, 32) 0.61 1570 (891, 3) 0.71 1651 (328, 131) 0.08 3212 (3, 124) 0.38 3249 (4, 91) 0.21 3575 (47, 34) 0.12 3623 (126, 90) 0.17

114

IR (Raman)

210

380

377s 397 ms

435 454

424 w 447 vs. 468 s

453 s

565

557 vs

599

665 w

651

681 ms

679

695 w

692

691 vs 726 w

775

795 vs

860

858 s

Anion (DTU)

Cal

Cal

104 (0.2, 0.1) 0.75 135 (1,3) 0.75 202 (9, 14) 0.62 369 (13, 0.4) 0.75 366 (2, 7) 0.32 429 (5, 19) 0.59 466 (3, 95) 0.31 687 (118, 1) 0.75 565 (12, 0.5) 0.75 656 (8, 2) 0.75 695 (10, 15) 0.56 632 (9, 0.3) 0.75 778 (22, 2) 0.75 821 (600, 4986) 0.33 986 (0.02, 0.7) 0.75 987 (72, 292) 0.28 1110 (1, 360) 0.28 954 (434, 6187) 0.34 1261 (31, 405) 0.36 1241 (28, 346) 0.32 1198 (23, 1227) 0.30 1344 (141, 515) 0.41 1425 (39, 0.33) 0.28 1526 (56, 159) 0.32 1437 (537, 5931) 0.33 1628 (226, 38) 0.73 3215 (5, 101) 0.53 3242 (17, 91) 0.22 3551 (99, 73) 0.10 3572 (131, 46) 0.47

72 (0.4,3) 0.75 120 (3,16) 0.75 201 (2, 14) 0.59 182 (21, 2) 0.75 376 (2,2) 0.74 416 (14, 3) 0.40 448 (29, 7) 0.58 445 (27, 2) 0.75 524 (38, 17) 0.75 633 (11, 7) 0.75 666 (0.3, 13) 0.49 554 (61, 1) 0.75 814 (14, 7) 0.75 834 (72, 5) 0.02 302 (4,5) 0.75 961 (44, 36) 0.48 1089 (151, 48) 0.29 975 (41, 67) 0.27 1271 (25, 76) 0.13 1176 (85, 90) 0.40 1121 (107,390) 0.23 1400 (53, 76) 0.18 1359 (27, 135) 0.62 1506 (53, 77) 0.54 1554 (532, 80) 0.24 1433 (90, 224) 0.09 3238 (16, 181) 0.27 3204 (4, 54) 0.69 3630 (43, 34) 0.65 3656 (34, 152) 0.09

Assignments

Raman

135

375

Cation (DTU+)

868 ms

938 966

984 s

1033

1076 w

1080 w

1074

1133 vvs

1125 vs

1158

1211 vs

1195 vs

1184

1231 vs

1200

1252 vs

1257 vvs

1301 1334

1384 w

1370 vs. 1433 vs

1425

1484 s

1495 vs

1499

1572 vvs

1577

1613 vs

3067

2896 s

3103

2930 w

3414

2996 s

3460

3081 s

1608 vs

/(ring) a00 /(ring) a00 opc b(CS) a0 /(ring) a00 ipc b(CS) a0 d(ring) a0 d(ring) a0 ipc c (NH) a00

c (CS) a00 c (CS) a00 m (ring) a0 breathing opc c (NH) a00 ipc c (CH) a00

mas(CS) a0 opc c(CH) a00 d(ring) a0 opc b(CH) a0

m (ring) a0 ipc b(CH) a0

ms (CS) a0 m (ring) a0 m (ring) a0 ipc b (NH) a0

m (ring) a0 opc b (NH) a0

m (C@C) a0 mas(CH) a0 ms(CH) a0 mas(NH) a0 ms (NH) a0

Calculated wave numbers below 1000 cm1 were scaled by the scale factor 0.9786 and those above 1000 cm1 by the scale factor 0.9550 for larger wave numbers. The experimental values corresponds to the only neutral DTU molecule. The first and second numbers within each bracket represent IR intensity (a.u.) and Raman activity while the numbers without bracket represent the corresponding calculated frequency and depolarization ratio of the Raman band respectively. vw: very-weak, w: weak, m: medium, ms: medium-strong, s: strong, vs: very-strong, vvs: very-very strong. *

a

NAH modes. The two NAH stretching modes (m30 and m29) could be identified as the calculated frequencies 3623 and 3575 cm1. The two IR bands 3081 and 2996 cm1 appear to correspond to the above two NAH stretching modes. The H atoms of both the NAH bonds vibrate in out-of-phase manner in the higher frequency

mode (m30) where as the two H atoms of both the NAH bonds vibrate in in-phase manner in the lower frequency mode (m29). The two NAH stretching modes for U, 2-TU and 4-TU were reported in the region 3415–3485 cm1 by Singh et al. [12]. The two NAH in-plane bending modes (m25 and m23) have been

R. Singh, R.A. Yadav / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 130 (2014) 188–197

calculated to be 1570 and 1397 cm1 both of which appear to be coupled with the CAH in-plane bending modes. These modes have been found experimentally at 1572 and 1384 cm1 with very strong and weak intensities respectively in the IR spectrum. The corresponding Raman bands observed at 1433 and 1370 cm1 appear with very strong intensities for m23 mode. Singh et al. [12] have assigned the two NAH in-plane bending modes for U, 2-TU and 4-TU in the region 1395–1455 cm1. The two out-of-plane NAH bending modes (m12 and m8) are pure modes and could be easily assigned at the calculated frequencies 707 and 578 cm1 with strong IR intensities but weak Raman activities. The Raman bands for these modes have been observed at 726 cm1 with weak and 557 cm1 with strong intensity. The H atoms of the two NAH bonds are vibrating in out of phase manner in case of the higher frequency mode and in in-phase manner in case of the lower frequency mode. The two out-of-plane NAH bending modes for U, 2-TU and 4-TU were reported earlier [12] in the range 550–700 cm1. C@S modes. The observed IR bands for the two C@S stretching modes (m20 and m14) could be identified as the frequencies 1231 and 858 cm1 which are observed with strong IR intensities while the Raman band for the lower mode (m14) only has been observed at 868 cm1. The higher frequency mode (m20) is calculated to be 1240 cm1 with the strong IR and Raman intensities while the calculated lower frequency mode (m14) 879 cm1 has very weak IR and Raman bands. The C@S stretching mode for the conducting molecules have been found at 948 and 1082 cm1 by Jaiswal et al. [29,30]. The two in-plane bending modes (m5 and m3) have been calculated to be 388 and 215 cm1 which are observed at the frequencies 397 cm1 in the IR spectrum. Both the C@S bonds bend in in-plane manner in case of the bending mode m5 and out of phase manner in case of the bending mode m3. The modes m5 and m3 were assigned by Singh et al. [12] for 2-TU and 4-TU at 269 and 271 cm1 respectively. The calculated C@S non-planar bending frequencies for the modes (m10 and m9) have been found to be 665 and 612 cm1 with very weak IR intensity and Raman activity. The observed IR band at 681 cm1 with medium strong intensity and the weak Raman band at 665 cm1 correspond to the calculated modes (m9) and (m10). The C@S non-planar bending mode was assigned in the range 725–760 cm1 for 2-TU and 4-TU by Singh et al. [12]. Radicals From the literature survey, it appears that these are only a few studies on the vibrational spectra of radical ions, e.g. Refs. [24– 25,31–32]. In this section the computed spectra of radical ions of DTU molecule are discussed. Radical cation. Ring modes. It is found that due to ionization of the neutral species into the cationic DTU radical the calculated vibrational frequency for the highest ring stretching mode (m26) decreases by 23 cm1 and depolarization ratio increases where as the IR intensity decreases slightly and Raman activity decreases by a factor of 4. This ring stretching mode is highly localized and appears to be pure C@C stretching mode. The Raman activity for the four ring stretching modes (m24, m22, m21 and m18) are found to increase by factors of 5, 25, 20 and 30 respectively. The calculated frequency for the ring stretching mode (m24) increases by 34 cm1 while the frequencies for the three ring stretching modes (m22, m21 and m18) decrease by 18, 59 and 271 cm1 respectively. The calculated frequency for the ring stretching mode (m11) is found to be unchanged compared to the neutral DTU molecule. The intensity of the calculated IR band increases by a factor of 9 and the Raman activity decreases by a factor of 2 for this mode. The ring in-plane

195

deformation modes (m16, m7 and m6) for DTU+ have calculated frequencies 987, 466 and 429 cm1 respectively which are found to be unchanged compared to the neutral DTU molecule. The IR intensity and Raman activity for the in-plane ring deformation mode (m16) is calculated to increase by factors of 4 and 146. In case of the deformation modes (m7 and m6), the IR intensity decrease by factors of 5 and 2 and the Raman activity increases by a factor of 9 in case of m7. The out-of-plane ring deformation modes (m4, m2 and m1) with the calculated frequencies 369, 135 and 104 cm1 have similar vibrational characteristics as for the DTU molecule. NAH modes. The calculated frequency of one (m30) of the two NAH stretching modes (m30 and m29) for DTU+ reduces by 51 cm1 and the Raman activity decreases by a factor of 2 with increased depolarization ratio. The NAH stretching frequency (m29) for DTU+ decreases by 24 cm1 with increase in the IR intensity and Raman activity by a factor of 2. The NAH in-plane bending mode (m25) is decreased by 133 cm1 while the NAH in-plane bending mode (m23) increases by 28 cm1. The NAH in-plane bending mode (m25) involves out-of-phase coupling whereas the NAH in-plane bending mode (m23) involves in-phase coupling of the two NAH planar bending vibrations. The out-of-plane NAH bending mode (m12) for the DTU+ ion is found to be lower by 75 cm1 with very weak IR and Raman band intensities. The calculated frequency for the NAH out-of-plane bending mode (m8) of DTU+ is found to increase by 109 cm1 and its IR intensity increases by a factor of 4. CAH modes. The calculated frequencies for the two CAH stretching modes (m28 and m27) of the DTU radical cation are found to be similar to those for the neutral DTU molecule. The in-phase coupled stretching mode (m28) found at higher frequency has increase in the IR intensity by a factor of 4. As a result of electron detachment the magnitude of the calculated vibrational frequencies for the two CAH in-plane bending modes (m19 and m17) increase by 48 and 28 cm1. For the higher frequency mode (m19) the intensity of the IR band is decreased by a factor of 5 while the Raman activity increases by a factor of 23. The H atoms of both the CAH bonds vibrate in in-phase manner in the higher frequency mode (m19) and in out-of-phase manner in case of the lower frequency mode (m17) for the DTU+ ion. The IR intensity for the lowest CAH in-plane bending mode decreases by a factor of 25 and the Raman activity increases by a factor of 24. Due to the radicalization, an increase of calculated frequency by 27 cm1 is noted for one (m15) of the two CAH out-of-plane bending modes of the DTU+ ion. It is noted that the vibrational frequency for the mode (m13) decreases by 14 cm1 for the DTU+ ion as compared to the neutral DTU molecule. It is found that the H atoms of both the CAH bonds vibrate in out of phase manner for the higher frequency mode m15 and in in-phase manner in case of the lower frequency mode (m13). C@S modes. The C@S stretching mode (m20) with higher frequency is found to have equal wavenumber for the cation as well as the neutral DTU molecule. The IR intensity for this mode (m20) decreases by a factor of 2 and Raman activity increases by a factor of 10. The C@S stretching mode (m14) with lower frequency has decreased wavenumber by 58 cm1 with increase of the IR intensity by a factor of 40 and greatly increased Raman activity. The in-plane bending mode arising due to the two C@S bonds is found at the frequency 366 cm1 with in-phase coupling (m5) and at 202 cm1 with out-of-phase coupling (m3). It can be seen that there are slight changes in the vibrational frequencies for the two C@S out-of-plane bending modes (m10 and m9) for the DTU cation as compared to the neutral molecule. Both the C@S non-planar bending modes are coupled with each other in in-phase manner for the higher frequency mode and in out of phase manner in case of the lower frequency mode. The magnitude of the calculated frequency

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for the mode (m9) decreases by 47 cm1 for the DTU+ ion due to the radicalization process. Radical anion. Ring modes. Due to the electron attachment, the C5@C6 bond of the DTU molecule loses its double bond character in the DTU anion radical. It can also be seen from the Table 3, that the calculated frequency for the C5@C6 bond stretching mode (m26) decreases by 218 cm1 and the IR intensity decreases by a factor of 3 while the Raman activity increases slightly for the anionic DTU species as compared to the DTU molecule. The Raman activities for the four ring stretching modes (m24, m22, m21 and m18) increase whereas for the lowest ring stretching mode (m11) it decreases. The calculated frequencies for the anionic DTU species and the neutral DTU molecule are nearly equal for the mode m24. The vibrational frequency for the mode m22 increases by 38 cm1 with slight increment in the IR intensity whereas that for the mode m18, it decreases by 150 cm1 with decreased in the IR intensity by a factor of 9 and increased Raman activity by a factor of 3. The lowest frequency mode (m11) assigned to the ring stretching mode decreases by 28 cm1 with increased Raman activity as compared to the neutral DTU molecule. The in-plane ring deformation modes (m16, m7 and m6) are found at the 961, 448 and 416 cm1. The highest frequency mode (m16) decreases by 26 cm1 with increased IR intensity and Raman activity by factors of 2 and 18 respectively. The second ring in-plane deformation mode (m7) has similar vibrational characteristics for the DTU ion as for the neutral DTU molecule while for the lowest ring in-plane deformation mode (m6) the calculated frequency decreases by 29 cm1 with decrease in Raman activity by a factor of 6. The calculated frequency for the highest ring out-of-plane deformation mode (m4) for the DTU anionic radical is 182 cm1 which is reduced by 201 cm1 as compared to the neutral molecule. The IR intensity decreases by a factor of 4 but Raman activity increases by a factor of 5. The outof-plane ring deformation mode (m2) shows slight increase in the IR intensity and Raman activity. The out-of-plane ring deformation mode (m1) assigned at the 72 cm1 for the DTU anionic radical decreases by 44 cm1 as compared to the DTU molecule. NAH modes. Similar to the cationic DTU radical the calculated frequencies for the two NAH stretching modes of the anionic radical have been assigned at higher frequencies (Table 3). Both of these stretching modes (m30 and m29) have been found to be in-phase and out-of-phase coupled modes. The calculated vibrational frequency for the in-phase coupled NAH stretching mode (m30) increases by 33 cm1 with decrease in IR intensity by a factor of 4 while the Raman activity increases by a factor of 2. The outof-phase coupled NAH stretching mode (m29) has increased frequency (55 cm1) with increased depolarization ratio. The two NAH in-plane bending mode frequencies (m25 and m23) assigned at the calculated frequencies 1554 and 1359 cm1 have increased Raman activities by factors of 26 and 6 where as the IR intensity slightly decreases for the higher (m25) NAH in-plane bending mode and increases by a factor of 3 for the lower (mm23) NAH in-plane bending mode. Both the NAH in-plane bending modes are also

coupled with each other and are coupled to the CAH in-plane bending modes also. The two NAH out-of-plane bending modes (m12 and m8) for the anionic DTU radical are found to be decreased in magnitudes by 153 and 133 cm1 compared to the neutral DTU molecule. These modes (m12 and m8) are also coupled with each other for the anionic DTU species contrary to the case of the DTU molecule. CAH modes. The CAH in-plane stretching mode (m28) frequency for DTU ion decreases by 45 cm1 and the Raman activity decreases by a factor of 2 with increase in the depolarization ratio as compared to the DTU molecule. The out-of-phase coupled CAH stretching mode (m27) frequency increases by 26 cm1 with increased IR intensity by a factor of 5 and slight decrease in the Raman activity. One (m19) of the two CAH in-plane bending modes increases by 58 cm1 with increased IR intensity and the Raman activity by factors of 6 and 4 for the DTU ion as compared to the DTU molecule. This mode (m19) appears to be coupled with the in-plane bending of the C5AH and N3AH bonds. The magnitude of the calculated frequency for the CAH in-plane bending mode (m17) is found to be nearly equal in magnitude to that of the DTU molecule with increased IR intensity and Raman activity by factors of 6 and 3 respectively. The mode (m17) is coupled with the N3AH in-plane bending mode. A drastic change (302 cm1) in magnitude of one (m15) of the two CAH out-of-plane bending modes (m15 and m13) is noticed for the DTU ion with strong IR intensity while the Raman activity increases by a factor of 2. This mode is assigned for the neutral DTU molecule at the calculated frequency 959 cm1. The lower CAH out-of-plane bending mode (m13) increases by 22 cm1, the IR intensity decreases by a factor of 2 and the Raman activity increases slightly as compared to its value for the neutral DTU molecule. The mode (m15) is in-phase coupled CAH out-of-plane bending mode for the anionic radical while for the DTU molecule the two CAH out-of-plane bending modes are uncoupled. C@S modes. The two C@S stretching mode frequencies (m20 and m14) are found to be decreased in magnitudes by 64 and 45 cm1 for the DTU ion in comparison to their values for the neutral DTU molecule. The C@S in-phase coupled stretching mode with the higher frequency has slight increase in the IR intensity while the Raman activity increases by a factor of 2. The out-of-phase coupled C@S stretching mode with the lower frequency has increased IR intensity while the Raman activity increases by a factor of 5 as compared to the neutral DTU molecule. The frequencies for the C@S in-plane bending modes (m5 and m3) do not show any change in magnitudes as compared to the neutral DTU molecule. In case of the out-of-phase coupled C@S in-plane bending mode the IR intensity decreases by a factor of 2 while the Raman activity increases by a factor of 2. The C@S in-phase coupled inplane bending mode has enhanced depolarization ratio. The two C@S out-of-plane bending modes (m10 and m9) are found to be decreased by 32 and 88 cm1 with strong IR intensity and Raman activity in the DTU ion as compared to the neutral DTU molecule.

Table 4 Some relevant parameters for DTU, DTU+ and DTU.

Total energies (Hartree) Zero-point vibrational energy (kcal/mol) Dipole moment (Debye) Constant volume molar heat capacity (CV) (cal/mol-K) Entropy (S) (cal/mol-K) Thermal Energy (E) (kcal/mol)

DTU

DTU+

DTU

1060.85590919 51.56578 4.9415 25.494 84.646 55.912

1060.54989549 50.86651 3.5203 25.933 86.706 55.302

1060.89516444 48.83428 5.5150 28.561 91.113 53.886

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Other spectroscopically important parameters

References

The total energies, dipole moments, zero-point vibrational energies and other relevant thermodynamic functions for the neutral DTU molecule and its radicals calculated at the B3LYP/6-311++G** level are collected in Table 4. The calculated dipole moment, Constant volume molar heat capacity (CV) and Thermal Energy (E) decrease whereas Entropy (S) at temperature (25.15 C) 298.15 K increases for the DTU+ ion. The calculated dipole moment, CV and S increases while E decrease for the DTU ion. The neutral DTU molecule is calculated to have lower energy as compared to the radical cationic molecule but higher energy than the anionic radical molecule. It can be seen that the stability of these species is in the order of DTU+ < DTU < DTU (Table 4).

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Conclusions Both the cationic and anionic radicals of the DTU molecule are found to be stable. The C5@C6 bond loses its double bond character as a result of anionic radicalization of the DTU molecule. Due to addition and removal of an electron the C4@S10 bond length increases while the C2@S8 bond length decreases due to removal of an electron and increases due to addition of an electron in the DTU molecule. Lengthening in the C5@C6 bond length and shortening in the C4AC5 bond length are noticed as a result of radicalization. The removal of an electron leads to increase the atomic charge on both the S and N atoms whereas addition of one electron leads to increase the atomic charges on the sites N1 and N3 while decrease the charges at the sites S8 and S10. It is found for the C@C stretching frequency decreases by 23 cm1 with decrease in the IR intensity as well as Raman activity and Raman band becomes strongly polarized due to cationic radicalization of the DTU molecule. One of the two CAH out-of-plane bending mode frequency decreases drastically by 657 cm1 in the DTU as compared to the neutral DTU molecule and its cationic species. All the calculated frequencies are found to be in good agreement with the experimental frequencies for the neutral DTU molecule.

Acknowledgements Two (RS and MK) of the authors are thankful to the Banaras Hindu University for the financial assistance in the form of fellowships. The authors are thankful to Prof. S.B. Rai and Dr. Ranjan K. Singh for providing the IR and Raman spectral data, respectively.