Vibrational modes study of thymine on the surface of copper electrode using SERS-measurement and the DFT method

Vibrational modes study of thymine on the surface of copper electrode using SERS-measurement and the DFT method

Journal of Molecular Structure 930 (2009) 60–64 Contents lists available at ScienceDirect Journal of Molecular Structure journal homepage: www.elsev...

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Journal of Molecular Structure 930 (2009) 60–64

Contents lists available at ScienceDirect

Journal of Molecular Structure journal homepage: www.elsevier.com/locate/molstruc

Vibrational modes study of thymine on the surface of copper electrode using SERS-measurement and the DFT method Zhiguo Shang a,b, Ying Gao c, Tingjian Jia a, Yujun Mo a,* a

Institute of Optics and Photoelectronic Technology, College of Physics and Electronics, Henan University, Kaifeng 475004, China The Graduate University for Advanced Studies, Myodaiji, Okazaki 444-8585, Japan c Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA b

a r t i c l e

i n f o

Article history: Received 26 February 2009 Received in revised form 23 April 2009 Accepted 27 April 2009 Available online 6 May 2009 Keywords: SERS Thymine DFT

a b s t r a c t The surface enhanced Raman scattering (SERS) spectra of thymine on copper electrode were recorded under different voltage values. Simultaneously, the chemical chelation was used to explain the interaction mechanism between thymine molecules and copper electrode. Moreover, the SERS spectrum of thymine was calculated with density functional theory (DFT). The frequency shifts between SERS and normal Raman spectra by experimental measurement were very approach to those obtaining by DFT method. The experimental results indicated that thymine molecules were adsorbed on the copper electrode through N1 and O7 with the chemical adsorption between [email protected] moiety and copper atoms. Ó 2009 Elsevier B.V. All rights reserved.

1. Introduction Surface enhanced Raman scattering (SERS) has a high sensitivity and specifically be applied to study the interaction between the organic molecules and the surfaces of transition metals. Since the SERS phenomenon was discovered [1,2], many nanophase materials have been designed with the purpose of obtaining strong vibration spectroscopy information of objective molecules. It was reported that the SERS enhancement factor of p-mercaptoaniline in the surface of Ag nanoshell films could reach up to 2.5  1010 [3]. Though SERS technique provides a useful tool to explain the structure of molecules adsorbed on metal surface, the enhancement mechanism is not completely clear. In the past years, many researchers have put different models, such as charge transfer [17–19] (chemical enhancement), plasmon-induced [20] or electromagnetic field effect [21] (physical enhancement), to explain the enhancement mechanism of SERS. However, these models can be only used to interpret some enhanced phenomena and none can explain all the enhanced phenomena perfectly [4–16]. Now density function theory (DFT) is accepted by most researchers as an effective tool for calculating the vibrational spectra of molecules. Concerning thymine molecules, Szczpaniak et al. [22] have calculated the spectrum of thymine in gas and Santamaria et al. [23] have assigned the vibrational mode of thymine by cal-

* Corresponding author. E-mail address: [email protected] (Y. Mo). 0022-2860/$ - see front matter Ó 2009 Elsevier B.V. All rights reserved. doi:10.1016/j.molstruc.2009.04.038

culation. But there are few reports about the theoretical study of SERS spectrum. As one of the nucleic acids of DNA, thymine takes a great role in gene and genome and the process of photosynthesis of plant is affected greatly by thymine. The molecular structure of thymine is shown in the Fig. 1(a). So far, thymine has been studied extensively from the biological function to chemical properties with the methods of experiment and theoretical calculation [24–32]. The SERS spectra of thymine on silver electrode and colloid were previously reported by since Koglin et al. [26,27]. Thereafter, the SERS spectrum of thymine on the silver and gold nanoparticle surfaces were also reported [28–31]. Rincon et al. reported the chelate process in Mg (II)–thymine complex by using theoretical calculation method [32], but they did not consider the relationship between this chelate process from the experimental results. Since enhancement mechanism of SERS is unclear, it is difficult to prove the detailed interaction mechanism and adsorbed state between thymine molecules and metal surfaces. In this paper, we designed two theoretical calculation models of SERS to explain the enhancement mechanism caused by chemical adsorption and calculated its Raman spectra. The theoretically calculated results presented that the thymine molecule was adsorbed on the copper electrode surface through N1 and O7 with the [email protected] chelate bond. The results showed acceptable agreement with experimental data. Moreover, the compared results indicated that the frequency shifts between SERS and normal Raman spectra by experimental measurements were very approach to those obtaining by DFT method.

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corded by Renishaw RM-1000 micro-Raman spectroscope. The rough copper electrode was prepared with the method of electrochemistry oxidation–reduction cycles (ORC) [34,35]. A rough copper film was prepared by mechanical polish. 0.1 mol/L KCl was used as electrolyte to meet the three poles, i.e., a comparing pole (calomel pole), an assistant pole (platinum ring) and a copper pole (copper film polished above), and all of them were connected to a constant potential instrument. A mixture of 0.1 mol/L KCl and 0.95  10 3 mol/L thymine aqueous solution (volume proportion 10:4) was added into the plating bath. The scan voltage was set from +0.4 V to 0.4 V. And the current was set as 500 mA. After scanning for three times, we got the copper pole with desired roughness and recorded the SERS spectra of thymine in situ through changing the voltages from 0 V to 0.8 V at excitation wavelength of 632.8 nm. 3. Discussion and results In our previous work, we already reported the theoretical calculation results of thymine molecules both in gas and crystal phase. And the assignment of vibrational modes of thymine and its SERS spectrum in silver colloids had been investigated [31]. The SERS spectra of thymine adsorbed on copper electrode under different voltages are shown in Fig. 4. There were few thymine molecules adsorbed on the rough copper pole when the voltage was 0 V. As the voltage decreased, the band 640 cm 1 (Wag N3AH) appeared at 0.4 V. Because the ring breath vibration was not enhanced, we considered the molecules were adsorbed on the copper pole in such way as the ring parallel orientation to the surface of copper pole. The SERS signal of thymine adsorbed on the surface of copper pole increased with the further decrease of voltage. The bands of 790, 1219, 1315, 1606 and 1652 cm 1 appeared at 0.6 V. Among these bands, the vibrational modes of 790 and 1219 cm 1 were related to ring breath [30]. The appearance of these bands indicated that the thymine ring was not parallel to the surface of copper, and there was certain angle between the thymine ring and copper surface. The band belonging to the vibration of metal-heteroatom (192 cm 1) [30] became clear and strong at 0.8 V. It suggested that the thymine molecules should be perpendicularly adsorbed on the surface of copper with the increase of voltage. The SERS theoretical calculation results are shown in Figs. 2 and 3. The band for the vibration of [email protected] (at 1672 cm 1 in the normal Raman spectrum) [30,31] appeared strongly at 1671 cm 1 in the model of [email protected] moiety chelation and at 1705 cm 1 in the model of

Fig. 1. (a) Molecular structure of thymine; (b) chelated structure of copper atom with thymine by [email protected]; (c) chelated structure of copper atom with thymine by [email protected]; (d) reasonable adsorption model of thymine on the surface of copper electrode at 0.8 V.

2. Experiment and calculation

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Our calculation was carried out with the software of Gaussian 03 [33]. In order to simulate the interaction between thymine molecule and copper electrode surface, two models were built as that thymine ion was chelated to a copper atom through N or O atom. The B3LYP complex function was used in our theoretical calculation and 6-31G basis sets were selected. In the same time, both diffused and polarization functions were added to heavy atoms. After the optimization of the configuration of the model, two reasonable and stable structures were presented, both of the copper atom were chelated with the [email protected] moiety (Fig. 1(b) and (c)). Then we calculated the Raman spectrum of the two model systems. The theoretically calculated Raman spectrum of the chelated system between thymine and copper atom was shown in Figs. 2 and 3. The crystal powder of thymine was purchased from Sigma and was of analytical grade. The Raman spectra of thymine were re-

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Wavenumber / cm-1 Fig. 2. Theoretical Raman spectrum of thymine molecule chelated with copper atom by [email protected] moiety.

Z. Shang et al. / Journal of Molecular Structure 930 (2009) 60–64

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Fig. 3. Theoretical Raman spectrum of thymine molecule chelated with copper atom by [email protected] moiety.

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Fig. 4. SERS spectra of thymine adsorbed on copper electrodes under different voltages in a 0.001 M thymine solution.

[email protected], and this band appeared at 1652 cm 1 in the SERS measurement. The band [email protected] appeared strongly at 1645 cm 1 in the model of [email protected] moiety chelation and at 1679 cm 1 in the model of [email protected], which appeared at 1606 cm 1 in the experiment. The bands at 1219, 1606 and 1652 cm 1 had been markedly enhanced in the experiment, which also showed strong intensity in the chelate model of [email protected] moiety. However, the band at 1219 cm 1 was very weak in the chelate model of [email protected] moiety. The band at 790 cm 1 was both strong in the experiment and the chelate model of [email protected] moiety, but it was weak in the chelate model of [email protected] moiety. All of the comparative results are shown in Table 1. Since the different chelated structure derive from the configuration optimization, some peak in the model of [email protected] moiety chelation is caused by N3AH and in the model of [email protected] is caused by N1AH. The comparative results presented that the model of [email protected] moiety chelation is more close to SERS theoretical calculation results. So that, we use this result to investigate the frequency shifts between SERS and normal Raman spectra in theory, and then compare with experimental results.

Comparing with the SERS spectrum in silver colloids, there was no new vibrational mode in the SERS spectrum of thymine on copper electrode. The band for the vibration of [email protected], which disappeared in the SERS spectrum from silver colloids, was enhanced in the SERS spectrum from copper electrode. The Raman shifts of [email protected] in the experiment and theoretical calculation had the same value of 20 cm 1. However, The band belonging to the vibration of [email protected] was shifted by 96 cm 1 from normal Raman spectrum to SERS spectrum in the experiment and the shift was 88 cm 1 in theoretical calculation. Our theoretical results presented that it was due to the chelation between O7 and copper atom. Thus, we confirmed that the thymine molecules were adsorbed on the copper electrode through N1 and O7 with [email protected] moiety (Fig. 1(d)). The frequency shifts between SERS and normal Raman spectra of thymine in the experiment and in the theoretical calculation are shown in Table 2. Except for some deflection of two bands (748 and 1490 cm 1 in normal Raman), the frequency shifts obtained by experiment and theoretical calculation methods are very

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Z. Shang et al. / Journal of Molecular Structure 930 (2009) 60–64 Table 1 Comparative results of SERS between experiment and theoretical calculation from two chelate models. No.

SERSa

Theoryb (error)

Theoryc (error)

Plane

Description of the SERS

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

192 w 640 w 767 w 790 s 823 s 996 s 1177 w 1219 s 1280 s 1350 s 1378 w 1451 w 1503 w 1606 s 1652 s

211 w (19) 670 w (30) 693 w (74) 776 w (14) 901 w (78) 976 w (20) 979 w (198) 1270 s (51) 1222 w (58) 1315 w (35) 1384 w (6) 1441 w (10) 1472 s (31) 1645 s (39) 1671 s (19)

131 w (61) 549 w (191) 709 w (58) 779 w (11) 732 w (100) 947 w (48) 996 w (181) 1196 w (23) 1334 w (54) 1393 w (43) 1442 w (64) 1455 s (4) 1640 s (137) 1679 s (73) 1705 s (53)

In Out In In In In Out In In In In In In In In

Stretch Cu-heteroatom (thymine) Wag N3/N1AH Dis R Dis R Dis R, wag C9AH10, C9AH11, C9AH12 Dis R, symmetry wag C9AH10, C9AH11, C9AH12 Dis R, wag C9AH10, C9AH11, C9AH12 Dis R, symmetry bend N3/N1AH, C5AC9 Dis R, anti-symmetry bend N3/N1AH, C6AH Anti-symmetry bend N3/N1AH, C6AH Dis R, symmetry bend N3/N1AH, C6AH Scissor C9AH10, C9AH12 Dis R Dis R, stretch [email protected] Dis R, stretch [email protected]

a

SERS spectrum of thymine molecules on the copper electrode at the voltage of 0.8 V. SERS spectrum of thymine molecules chelated with copper by [email protected] moiety from theoretically calculation method. c SERS spectrum of thymine molecules chelated with copper by O[email protected] moiety from theoretically calculation method. ‘Dis R’ is the mode of ring distortion, ‘w’ is for ‘weak signal’ and ‘s’ is for ‘strong signal’. b

Table 2 Experimental data compared with the theoretical calculated data. No.

SERSa

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

192 w 640 w 767 w 790 s 823 s 996 s 1177 w 1219 s 1280 s 1350 s 1378 w 1451 w 1503 w 1606 s 1652 s

NRSb 616 748 765 804 984 1215 1260 1247 1368 1377 1459 1490 1702 1672

Differencec

SERSd

24 19 25 19 12 38 41 33 18 1 8 13 96 20

211 w 670 w 693 w 776 w 901 w 976 w 979 w 1270 s 1222 w 1315 w 1384 w 1441 w 1472 s 1645 s 1671 s

NRSe 650 707 732 873 983 1028 1322 1184 1350 1368 1444 1636 1733 1691

Differencef

Plane

Description of the SERS

20 14 44 28 7 49 52 38 35 16 3 164 88 20

In Out In In In In Out In In In In In In In In

Stretch Cu-heteroatom (thymine) Wag N3AH Dis R Dis R Dis R, wag C9AH10, C9AH11, C9AH12 Dis R, symmetry wag C9AH10, C9AH11, C9AH12 Dis R, wag C9AH10, C9AH11, C9AH12 Dis R, symmetry bend N3AH, C5AC9 Dis R, anti-symmetry bend N3AH, C6AH Anti-symmetry bend N3AH, C6AH Dis R, symmetry bend N3AH, C6AH Scissor C9AH10, C9AH12 Dis R Dis R, stretch [email protected] Dis R, stretch [email protected]

a

SERS spectrum of thymine molecules on the copper electrode at the voltage of 0.8 V. NRS spectrum from experiment method. c The frequency shifts between SERS and normal Raman spectra of thymine in the experiment. d SERS spectrum of thymine molecules chelated with copper from theoretically calculation method. e NRS spectrum from theoretically calculation method. f The frequency shifts between SERS and normal Raman spectra of thymine in the theoretical calculation. ‘Dis R’ is the mode of ring distortion, ‘w’ is for ‘weak signal’ and ‘s’ is for ‘strong signal’. b

close. These explained the Raman shifts were derived from the chelation of [email protected] moiety. Therefore, it was concluded that the thymine molecules were adsorbed on the surface of copper electrode through N1 and O7 with the chemisorption between [email protected] moiety and copper atoms. 4. Conclusions The comparative results of SERS spectrum between two theoretical calculation models and experiment present that thymine molecules were adsorbed on the surface of copper electrode with the chelation of [email protected] moiety with copper atoms. The remarkable agreement of Raman shifts obtained by experiment and theoretical calculation methods provides us an efficient method to analyze the configuration information of molecule when adsorbed on metal surface. Acknowledgement This work was supported by National Science Foundation of China (No. 10674041).

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