UV, IR, and Charge Transfer SERS Spectra - ACS Publications

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A Theoretical Spectroscopic Study on the Au, Ag, Au/Ag, and Ag/Au Nanosurfaces and Their Cytosine/Nanosurface Complexes: UV, IR, and Charge Transfer SERS Spectra Hossein Farrokhpour, and Maryam Ghandehari J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.9b00683 • Publication Date (Web): 07 Jun 2019 Downloaded from http://pubs.acs.org on June 7, 2019

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The Journal of Physical Chemistry

A Theoretical Spectroscopic Study on the Au, Ag, Au/Ag, and Ag/Au Nanosurfaces and Their Cytosine/Nanosurface Complexes: UV, IR, and Charge Transfer SERS Spectra

Hossein Farrokhpour* and Maryam Ghandehari Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran

Corresponding Author: Hossein Farrokhpour E-Mail: [email protected]; [email protected]

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ABSTRACT The first part of this work is related to the calculation of the absorption spectra of pure Ag and Au nanosurfaces, bimetallic nanosurfaces composed of Ag and Au metals (Au/Ag and Ag/Au) and the nanosurfaces interacted with cytosine (CYT/Au, CYT/Au/Ag, CYT/Ag and CYT/Ag/Au). Comparison of the absorption spectra and changes in the total and partial density of states (TDOS and PDOS) of the systems allowed the effect of metallic structure of the sublayer and adsorbate on the intensity and position of the maximum of the spectra to be explored. The absorption lines responsible for the charge transfer from the CYT to nanosurfaces due to the electronic excitation for each CYT/nanosurface were determined and the effect of sublayer on these electronic transitions was studied. In the second part of this work, the effect of metallic structure of sublayer on the IR spectrum of the CYT adsorbed on the Au/Ag and Ag/Au nanosurfaces was studied and the vibrational bands of the CYT that were sensitive to the metallic structure of sublayer were determined. In addition, the frequency-dependent Raman spectra of the CYT adsorbed on the selected nanosurfaces were calculated at several wavelengths corresponding to electronic excitation charge transfer from the CYT to the nanosurface. The vibrational bands of the CYT showing the intensity enhancement due to the charge transfer in the Raman spectrum for each nanosurface were determined. The theoretical spectroscopic results presented in this work are very useful for the interpretation of experimental results especially when the CYT is adsorbed on nanosurfaces such as Ag, Au and their bimetallic nanosurfaces.


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Introduction Metal nanostructures in the form of nanoparticles, nanosurfaces, and nanoclusters, especially those composed of Au and Ag, are the most common candidates in biology and biomedical applications for designing of nanosensors and drug delivery nanocarrier systems.1 The reason for using Ag and Au metals for constructing nanostructures compared to other metals is due to their localized surface plasmon resonance (LSPR), which are located in the visible region and near infrared region2,3, and their biocompatibility properties.4 Also, Ag and Au metals are the most intensively investigated surface-enhanced Raman scattering (SERS) metals.5-15Besides much attention to pure Au and Ag nanostructures, there is much interest to bimetallic nanostructures (core-shell and alloy structures) composed of Ag and Au16-27 due to their much higher LSPR intensity compared to pure Au nanostructures and their greater chemical stability compared to pure Ag nanostructures.16 Also, the electrical, optical and catalytic properties of the bimetallic nanoparticles composed of Au and Ag are strongly dependent on the composition and arrangement of metal atoms. Three kinds of bimetallic nanoparticles composed of Ag and Au have been synthesized including AgcoreAushell, AucoreAgshell and alloyed AgAu. 19-21,23 Among the biological molecules, the interaction of DNA with metal nanostructures constructed from noble metals (Au, Ag and Cu) is the subjects of great interest in various fields such as biotechnology and nanotechnology. 28-38 To explore the mechanism of interaction of DNA with metal nanostructures, the study of the adsorption of isolated DNA bases on metal nanostructures is a promising approach. This is because the knowledge about the fundamental modes of metal interaction with a simple DNA base would greatly enhance our understanding of how metals interact with more complex nucleic acid structures such as DNA. There are different experimental and theoretical papers in literature related to the interaction of isolated DNA bases



with nanostructures including nanoparticles, nanosurfaces, and nanoclusters of noble metals and their bimetallic nanostructures.39-50 In the experimental papers, different spectroscopic techniques including UV, IR, and SERS have been used to study the adsorption of DNA bases on the nanostructures. The displacement of the position of LSPR of metal nanostructure in the UV spectrum due to the interaction between nanostructure and adsorbate and change in its intensity have been used as a tool for sensing of DNA bases with nanostructures. The IR and SERS spectra have been employed to obtain information about the adsorption geometry of DNA bases on the surface of nanostructures.51-76 In continuation of our previous work,40 two aims are followed in this paper. (i) The absorption spectra of bare Au, Ag, Au/Ag, and Ag/Au nanosurfaces were calculated and compared with each other to see the effect of sublayer on the absorption spectra. Although there are published papers in literature on the synthesis of pure and bimetallic nanostructures of these metals and their characterizations based on the variations in their absorption spectra, the theoretical studies to interpret these variations are very limited. In this work, theoretical calculations were conducted to interpret and explain these variations. (ii) Although the adsorption of DNA bases on metal nanosurfaces and nanoparticles have been studied theoretically in literature, these studies mainly focused on the calculation of adsorption energy, adsorption geometry, charge transfer and mixing of molecular orbitals of metal nanostructure with those bases. In addition, theoretical studies of their absorption, IR and Raman spectra is very limited. In our previous work,40 the adsorption of cytosine (CYT) on pure Ag and Au nanosurfaces (CYT/Ag and CYT/Au), and Ag/Au and Au/Ag bimetallic nanosurfaces (CYT/Ag/Au and CYT/Au/Ag) were studied and the effect of sublayer on the adsorption of CYT on these nanosurfaces was investigated. In this work, the absorption spectra of these systems along with the IR and SERS spectra of CYT adsorbed on the nanosurfaces were


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calculated and compared with each other to see how the metallic structure of sublayer changes these spectra. The SERS spectra of the CYT were calculated at wavelengths corresponding to the charge transfer (electron transfer) from the CYT to nanosurface due to the electronic excitation. The vibrational modes of the CYT showing intensity enhancement in the calculated SERS spectra were determined. It is important to note that this is the first theoretical report on the SERS spectra of the CYT adsorbed on metal nanostructure due to only charge transfer from it to the substrate.

Computational details The initial structures of bare nanosurfaces and CYT/nanosurface complexes of this work were constructed by reducing the size of their corresponding optimized structures reported in our previous study.40 The detailed information about the construction and optimization of clean nanosurfaces and CYT/nanosurface structures have been given in our previous paper [40] (see section 2 and Figure 1, S1 and S2 in reference 40). However, some brief explanations have been given in supporting information. The size of the optimized nanosurfaces and CYT/nanosurface complexes in our previous work40 were so big for calculating the UV, IR and SERS spectra, that these calculations were nearly impossible. Therefore, reducing the size of the nanosurfaces was proposed. Figure 1a shows the structure of CYT/Au/Ag complex taken from reference 40. The size of the optimized structures reported in reference 40 was reduced so that the number of metal atoms decreased from 224 to 76 atoms. It is important to note that, the size reducing was performed without any change in the position and orientation of the CYT on the nanosurfaces. To check the validity of the reduced CYT/nanosurface structures with respect to the location of their local minima on the potential energy surface, frequency calculation was performed for each reduced CYT/nanosurface using the method of optimization in our previous work40 (see supporting



information). No imaginary vibrational frequencies were observed which meant that the reduced structures were still at the minimum of the potential energy surface of the new structures. Further optimization was performed on the reduced CYT/nanosurface structures in the form of a small deviation of the orientation of the CYT from its optimized orientation in the unreduced CYT/nanosurfaces in our previous work40. In this optimization all of the metal atoms of the reduced nanosurface were rigid except for the metal atoms of the first layer. After optimization, it was observed that the orientation of the CYT in the reduced CYT/nanosurface structures was nearly same as those obtained in our previous work40. Therefore, it was concluded that the reduced CYT/nanosurface systems can be considered an alternative candidate to the big structures reported in our previous work40. Figure 1b shows the optimized structure of the reduced CYT/Au/Ag structure from three different views. For more information about the theoretical method used for the optimization see supporting information. The absorption spectra of the reduced clean nanosurfaces and CYT/nanosurface structures were calculated by the time-dependent density functional theory (TD-DFT) method in the twolayer “our own n-layered integrated molecular orbital and molecular mechanics” (ONIOM) scheme considering 150 excited states in the calculation employing M06-L functional78. The 6311++G(d, p) and LANL2DZ basis sets were used for the CYT and metal atoms in the quantum mechanics (QM) region, respectively, and the metal atoms in molecular mechanics (MM) region were described using universal force field (UFF) (see Figure 1). The IR and normal Raman spectra (static Raman spectra) of the CYT/nanosurface were calculated at the same level of theory using DFT method. Also, the frequency-dependent near resonance Raman (FDNRR) spectra of CYT were calculated at the wavelengths near the resonance of the electronic excitations corresponding to the charge transfer from the CYT to surface using the infinite-lifetime approximation employing


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TD-DFT method. In the FDNRR spectrum, the relative intensities of vibrational bands were the same as the SERS spectrum recorded at a wavelength equal to the resonance of the electronic excitation.79 Therefore, all of the FDNRR spectra calculated in this work are called SERS spectra throughout this paper. All of the calculations were performed using Gaussian 09 (G09) quantum chemistry package.80 The plots of total and partial density of states (TDOS and PDOS, respectively) were calculated using Multiwfn 3.4 software.81

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Figure 1. (a) The optimized structure of the CYT/Au/Ag complex taken from reference 40. (b) The optimized reduced structure of the CYT/Au/Ag complex from three views. The yellow and blue colors show the Au and Ag metal atoms, respectively. The balls and dots show the atoms in the QM and MM regions, respectively, in the ONIOM scheme.



Results and discussion (a) Absorption spectra of clean nanosurfaces There are several experimental papers in the literature on the synthesis of nanostructures composed of Au and Ag metals. Fan et al. synthesized pure Ag and Au nanoparticles and their alloys with the size of 3-5 nm.82 They observed that as the percentage of Ag increased in the bimetallic alloy nanoparticle the maximum of absorption spectrum shifted from 530 nm for pure Au to 400 nm for pure Ag and the composition of the alloy bimetallic nanoparticles was monitored through the absorption spectroscopy. Mott et al. synthesized pure Ag nanoparticles and coated them with a layer of Au with the average size of 20 nm.19 They found that as the thickness of Au layer increased the intensity of the absorption spectrum decreased and shifted to the higher wavelength. Adhyapak et al. synthesized pure Ag and Au nanoparticles and their bimetallic forms including AgAu alloy, AgcoreAushell, and AucoreAgshell nanoparticles and compared their absorption spectra with each other.83 Shmarakov et al. compared the antitumor activity of Au, Ag, AucoreAgshell and AgcoreAushell nanoparticles.84 They observed that the presence of Au as core shifted the absorption spectrum of AucoreAgshell to higher wavelength compared to pure Ag nanoparticles while the reverse trend was seen for AgcoreAushell nanoparticles compared to Au nanoparticles. Hu et al. synthesized Ag-Au bimetallic nanoparticles in the forms of alloy and core-shell and recorded their time-dependent absorption spectra.27 In addition, they used discrete dipole approximation to simulate the absorption spectra of structures based on the Mie theory.85 Their simulations showed that as the percentage of Ag as shell increased, the intensity of absorption spectrum increased and shifted to the lower wavelength. Li et al.21 synthesized three types of bimetallic nanoparticles including AgcoreAushell, AucoreAgshell and alloyed AgAu with the mean size of 4-5 nm and recorded their absorption spectra at different mole ratio of Ag and Au in the nanoparticle. They showed that the


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presence of Au metal as the core in the AucoreAgshell nanoparticle with 1:1 mole ratio caused the maximum of its absorption spectrum (505.00 nm) to be located at a higher wavelength compared to pure Ag nanoparticles (460.00 nm). Kuladeep et al.23 synthesized the Au-Ag alloy nanoparticles with laser ablation and followed the variation in the absorption spectrum of nanoparticle while changing the percentage of Au and Ag in the metal nanoparticle. Samal et al.86 proposed a simple and efficient methodology for the size-tunable synthesis of AucoreAgshell nanoparticles and recorded their absorption spectra along with the calculation of the absorption spectra using Mie theory. The calculated absorption spectra of clean nanosurfaces including (Ag and Ag/Au) and (Au and Au/Ag) have been demonstrated in Figures 2 and 3, respectively. As can be seen in Figure 2, the presence of Au sublayers in the Ag/Au nanosurface increases the intensity of absorption spectrum considerably, and shifts the spectrum to higher wavelength compared to the Ag nanosurface. The calculated position of the maximum of the absorption spectrum of Ag and Ag/Au nanosurfaces are 492.26 and 526.03 nm, respectively, which shows that the Au sublayers shift the absorption spectrum 33.7 nm to a higher wavelength. It is important to note that the shift of the position of the maximum absorption spectrum of Ag/Au nanosurface compared to pure Ag nanosurface is similar to what has been observed, experimentally, for AucoreAgshell nanoparticles compared to pure Ag nanoparticles of the same size.21 The position of the maximum of absorption spectrum of Ag and Ag/Au nanosurfaces from the current study is approximately 32 and 21 nm higher in wavelength, respectively, compared to the absorption spectrum of Ag and AucoreAgshell nanoparticles reported by Li et al.21 In Figure 3, the presence of Ag metal as a sublayer in the Au/Ag nanosurface showed the reverse trend so that the maximum of the absorption spectrum of Au/Ag nanosurface shifted to a lower wavelength compared to Au nanosurface and its intensity increases. This behavior is in



agreement with the comparison of the experimental absorption spectra of Au and AgcoreAushell (with 1:1 mole ratio) nanoparticles reported by Li et al.21 The calculated position of the maximum of absorption spectrum of pure Au and Au/Ag nanosurfaces are 614.43 and 511.65 nm, respectively, and the experimental values reported by Li et al.21 for the Au and AgcoreAushell nanoparticles are 540.00 and 512.50 nm, respectively. For more confirmation, Shmarakov et al.84 have recorded the absorption spectra of Ag, Au, AucoreAgshell, and AgcoreAushell nanoparticles. They showed that the presence of Au as core shifted the maximum of the absorption spectrum of AucoreAgshell nanoparticles to a higher wavelength compared to Ag nanoparticles while using Ag metal as a core in the AgcoreAushell nanoparticles shifted the maximum of absorption spectrum to a lower wavelength. Although, the absorption spectra of the Ag, Au, AucoreAgshell, and AgcoreAushell nanoparticles have not been calculated in the current study, the trend in absorption spectra of the nanosurface with metalic sublayer calculated in this study are in agreement with their corresponding experimental pure and core-shell nanoparticles in the litrature. similar to what has been observed for the corresponding nanoparticles, experimentally in literature. The other important point is that the position of the LSPR for a metal nanostructure depends considerably on its shape, size, the environment of the nanostructure. Therefore, it should not be expected that the calculated LSPR positions would exactly match the values of their corresponding nanoparticles. The insets of Figures 2 and 3 show the oscillator strengths of the electronic transitions versus wavelength for the absorption spectra. It is seen that the presence of Au sublayer in the Ag/Au nanosurface increases the number of allowed electronic transitions compared to the Ag nanosurface, especially in the range of 480 to 560 nm. This increase caused the shift of the maximum of the absorption spectrum of Ag/Au nanosurface to higher wavelength compared to the Ag nanosurface. Similarly, the inset of Figure 3 shows that the presence of Ag sublayer in the


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Au/Ag nanosurface increases the allowed electronic transitions in the range of 500 to 600 nm compared to Au. It can be concluded that the allowed transitions shift to the lower wavelength in the Au/Ag nanosurface compared to the Au nanosurface showing that the separation between the occupied and unoccupied states has been increased in Au/Ag nanosurface. Comparison of the inset of Figure 2 with that of Figure 3 shows that the increase in the number of allowed electronic transitions of a bimetallic nanosurface compared to its pure nanosurface for Ag/Au is considerably more than that for Au/Ag nanoaurface.



CYT/Ag/Au Au_Ag_CY 25 CYT/Ag/Au

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Figure 2. The calculated UV absorption spectra of clean nanosurfaces including Ag (blue spectrum) and Ag/Au (black spectrum) along with the calculated UV spectra of the complexes of cytosine (CYT) with Ag (CYT/Ag ; red spectrum) and Ag/Au (CYT/Ag/Au ; green spectrum). The inset shows the oscillator strengths of the electronic transitions of each UV spectrum.


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Figure 3. The calculated UV absorption spectra of clean nanosurfaces including Au (blue spectrum) and Au/Ag (black spectrum) along with the calculated UV spectra of the complexes of cytosine (CYT) with Au (CYT/Au ; red spectrum) and Au/Ag (CYT/Au/Ag ; green spectrum). The inset shows the oscillator strengths of the electronic transitions of each UV spectrum.



Comparison of the TDOS and PDOS of the bimetallic nanosurfaces with pure ones provides useful information about the effect of sublayer on the occupied and unoccupied states. Figure 4a shows the calculated TDOS and PDOS of Ag/Au nanosurface and compares them with the TDOS of pure Ag nanosurface. It is seen that the TDOS of Ag nanosurface (green plot) shows a strong peak located at -8.11 eV related to the occupied molecular orbitals. The presence of Au sublayer in the Ag/Au nanosurface causes that the intensity of this peak to decrease (see the black curve in Figure 4a) considerably, and its position to slightly shift to a more negative energy (-0.33 eV). This intensity decrease shows that the energy separation between occupied orbitals has been increased in the Ag/Au compared to Ag nanosurface. On the other hand, the TDOS of Ag/Au nanosurface is nearly same as the DOS of Ag nanosurface in the range of -2.50 to 7.50 eV with the slight decrease in its intensity indicating that the number of unoccupied states has been slightly decreased in this energy region for Ag/Au nanosurface. Also, there is an increase in the number of the unoccupied states in the region between 7.50 and 20 eV for the Ag/Au nanosurface compared to Ag nanosurface while, a decrease is seen in the number of unoccupied states for the Ag/Au nanosurface compared to Ag nanosurface for the energies higher than 20 eV. Based on Figure 4a, the main effect of the Au sublayer is the decrease of the density of states of occupied states and shifting them to the lower energy. Based on the comparison of TDOS of Ag/Au nanosurface with that of Ag surface, it is expected that the maximum of absorption spectrum of Ag/Au should slightly shift to the lower wavelength while the reverse trend is seen in Figure 2. Therefore, it can be concluded that the main reason for the shift of the maximum of absorption spectrum of Ag/Au nanosurface to higher wavelength is the allowance of many electronic transitions which were forbidden for Ag nanosurface. It should be noted although the number of Au atoms in the Ag/Au nanosurface is three times more than Ag atoms, the PDOS of Ag fragment


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(red curve in Figure 4a) is comparable with that of Au fragment (blue curve). The contribution of Au fragment in the occupied and unoccupied states of Ag/Au nanosurface is greater than Ag fragment. Figure 4b shows the calculated TDOS and PDOS of Au/Ag nanosurface and compare them with the DOS of pure Au nanosurfaces. It is seen that the contribution of Ag sublayers in the occupied molecular orbitals is considerably greater than the contribution of Au layer based on the comparison of the PDOS of Au (blue curve) and Ag fragments (red curve) in the range of -10 to 5 eV. Comparison of Figure 4b with 4a shows that the contribution of sublayer in the occupied molecular orbitals of the Au/Ag nanosurface is considerably greater than that in the Ag/Au nanosurface. Also, it is seen that the intensity of the peak of TDOS related to the occupied states of Au/Ag increases compared to pure Au surface and shifts to more negative energy (-0.79 eV) and its width decreases. This observation is opposite to what was observed for the TDOS of Au/Ag nanosurface compared to DOS of pure Ag nano surface. The increase of the intensity of TDOS of Au/Ag compared to Au in the range of -10 to -5 eV shows that the occupied states of the Au/Ag nanosurface become closer to each other compared to Au nanosurface. The TDOS of Au/Ag nanosurface, in the range of -2.5 to 7.5 eV related to the unoccupied states, increases slightly compared to Au nanosurface. Since, the occupied states of Au/Ag nanosurface shifts to more negative energies and the change in the DOS of its unoccupied states in the range of -2.5 to 7.5 eV is very small, it can be concluded that the energy separation between the occupied and unoccupied states increases in Au/Ag nanosurface and its absorption spectrum should shift to the lower wavelength compared to Au nanosurface which is in agreement with what has been shown in Figure 3.



Density of of states (states/eV) Density states (DOS)

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Energy (eV) Figure 4. (a) The calculated total density of states (TDOS) of Ag and Ag/Au nanosurfaces along with the partial DOS (PDOS) of the Au and Ag fragments of the Ag/Au nanosurface. The solid and dashed lines show the energy position of the HOMO of Ag/Au and Ag nanosurfaces, respectively. (b) The calculated TDOS of Au and Au/Ag nanosurfaces along with the PDOS of the Au and Ag fragments of the Au/Ag nanosurface. The solid and dashed lines show the energy position of the HOMO of Au/Ag and Au nanosurfaces, respectively.


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(b) Absorption spectra of CYT/Ag/Au, CYT/Au/Ag, CYT/Ag, and CYT/Au Figures 2 and 3 also showed the calculated absorption spectra of CYT+nanosurface complexes (CYT/Ag/Au, CYT/Ag, CYT/Au/Ag, and CYT/Au). It was seen that the presence of CYT on the nanosurfaces shifted their absorption spectra to higher wavelength. The presence of CYT on the Ag nanosurface shifted the maximum of its spectrum to higher wavelength approximately 13 nm compared to the spectrum of clean Ag nanosurface. The corresponding shift for the CYT/Ag/Au complex was approximately 9 nm compared to clean Ag/Au nanosurface. It can be seen that the presence of Au as a sublayer decreased this wavelength shift. The magnitude of this shift for the CYT/Au complex compared to clean Au nanosurface was 9 nm and the presence of Ag as a sublayer in the CYT/Au/Ag complex increased the magnitude of this shift to 34 nm compared to clean Au/Ag nanosurface. It was seen that the Ag sublayer increased this shift in the CYT/Au/Ag complex compared to that in the CYT/Au complex while when Au was used as the sublayer in the CYT/Ag/Au complex, this shift was less in magnitude in comparison with the CYT/Ag complex. The other important point is that the presence of the CYT in the CYT/Ag/Au complex increased the intensity of absorption spectrum compared to clean Ag/Au nanosurface while the opposite trend was seen in the CYT/Au/Ag compared to Au/Ag nanosurface. Figure 5a compares the TDOS of CYT/Ag/Au complex and the PDOS of Ag and Au in this structure with those of the clean Ag/Au to see the effect of the CYT on the contribution of Au and Ag fragments in the TDOS of the CYT/Ag/Au. As seen, the adsorption of CYT on Ag/Au nanosurface caused the increase of PDOS of Au in the range of 0 to 10 eV while the PDOS of Ag decreased in this range compared to those in the Ag/Au nanosurface. This meant that the presence of CYT in CYT/Ag/Au increased the contribution of Au fragments in the unoccupied states in the range of 0 to 10 eV. Also, it was seen that there is no change in the PDOS of Ag and Au in the



energy range related to the occupied states (below -5 eV) due to the presence of CYT. The adsorption of the CYT on the Ag/Au nanosurface caused the increase of the TDOS of the CYT/Ag/Au complex compared to that of clean Ag/Au nanosurface in the energy range higher than 0 eV related to the unoccupied states which meant that the number of unoccupied states of CYT/Ag/Au complex is more than that of Ag/Au nanosurface in this energy region. The reason for this increase was due to the mixing of the unoccupied states of Ag/Au nanosurface with the unoccupied states of CYT which was accompanied with the increase in the number of states of CYT/Ag/Au complex compared to that of Ag/Au nanosurface in this energy region. The increase of the number of unoccupied states of CYT/Ag/Au complex caused the decrease of the energy gap between its unoccupied states compared to Ag/Au nanosurface. In this case, it was expected that the number of electronic transitions from the occupied states to unoccupied states increased in the CYT/Ag/Au complex compared to clean Ag/Au nanosurface. This increase has also been shown in the inset of Figure 2 so that the number of allowed electronic transitions of the CYT/Ag/Au complex were considerably greater than those of the Ag/Au nanosurface. In fact, the presence of CYT in the CYT/Ag/Au complex increased the number of allowed electronic transitions, especially in higher wavelengths compared to Ag/Au nanosurface and led to the increase of the intensity of the absorption spectrum of the CYT/Ag/Au complex compared to the spectrum of Ag/Au nanosurface, as shown in Figure 2. The presence of the CYT in the CYT/Au/Ag complex did not induce significant changes in the PDOS of Ag and Au compared to those of clean Au/Ag nanosurface (see Figure 5b). This meant that the contribution of Au and Ag fragments in the states of the CYT/Au/Ag complex was not as affected by the interaction of CYT with the Au/Ag nanosurface unlike to what was observed for the CYT/Ag/Au complex compared to Ag/Au nanosurface in Figure 5a. Figure 5b also shows


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that the presence of the CYT in the CYT/Au/Ag complex increased the TDOS of the complex in the energy region of 0 to 40 eV compared to clean Au/Ag nanosurface. This meant that the number of unoccupied states of the CYT/Au/Ag complex was more than the number of unoccupied states of Au/Ag nanosurface in this energy region due to the mixing of the states of CYT with the states of nanosurface. The increase of the unoccupied states in the CYT/Au/Ag complex was accompanied with the increase of allowed electronic transitions compared to clean Au/Ag surface. The inset of Figure 3 shows the increase of allowed transitions of the CYT/Au/Ag complex compared to Au/Ag nanosurface for the wavelengths higher than 550 nm which led to the shift of the absorption spectrum of the CYT/Au/Ag complex to the higher wavelength. It is important to note that although the presence of CYT in the CYT/Au/Ag complex increased the number of allowed transitions, it decreased the oscillator strength of some transitions which in turn led to the decrease of the intensity of its absorption spectrum compared to the spectrum of Ag nanosurface. Figure 2 also compares the absorption spectrum of Ag nanosurface with that of CYT/Ag complex. It is seen that the intensity of absorption spectrum of CYT/Ag complex increased and the maximum of absorption spectrum shifted to the higher wavelength compared to clean Ag nanosurface. The inset of this figure showed that the presence of CYT increased the number of allowed transitions of the CYT/Ag complex. Figure 6a compared the DOS of Ag nanosurface with the TDOS of CYT/Ag complex. It was seen that the presence of CYT increased the TDOS of CYT/Ag complex in the energy region of unoccupied states which was in agreement with the increase of the intensity of absorption spectrum of the CYT/Ag complex compared to Ag nanosurface. Also, it was seen that the PDOS of Ag in the CYT/Ag complex was nearly matched to the DOS of clean Ag nanosurface. In the case of Au nanosurface and CYT/Au complex, the increase of the intensity of the absorption spectrum of CYT/Au complex and its shift to the higher



wavelength compared to the spectrum of Au nanosurface were small (see Figure 3).Similar to CYT/Ag, the adsorption of CYT on the Au nanosurface increased the DOS of the unoccupied states compared to Au nanosurface (see Figure 6b).


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Density of states (states/eV)

(a) TDOS of CYT/Ag/Au TDOS of Ag/Au PDOS of Au fragment PDOS of Ag fragment PDOS of CYT fragment

Energy (eV) (b)


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


TDOS of CYT/Au/Ag TDOS of Au/Ag PDOS of Ag fragment PDOS of Au fragment

PDOS of CYT fragment

Energy (eV) Figure 5. (a) The calculated total density of states (TDOS) and partial DOS (PDOS) of the CYT/Ag/Au complex (dashed line curves) and Ag/Au nanosurface (solid line curves). (b) The calculated TDOS and PDOS of the CYT/Au/Ag complex (dashed line curves) and clean Au/Ag nanosurface (solid line curves).



(a)


10

TDOS of CYT/Ag PDOS of Ag PDOS of CYT DOS of Ag

8 6

4 2 0

-10

0

10

20

30

40

Energy (eV) Density of states (states/eV)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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8

(b)

TDOS of CYT/Au PDOS of Au PDOS of CYT DOS of Au

6

4

2

0 -10

0

10

20

30

40

Energy (eV) Figure 6. (a) The calculated total density of states (TDOS) and partial DOS (PDOS) of CYT/Ag and clean Ag nanosurface. (b) The calculated TDOS and PDOS of CYT/Au and clean Au nanosurface.


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(c) The effect of sublayer on the charge transfer electronic transitions In this part, the effect of sublayer on the charge transfer electronic transitions in the calculated absorption spectra is discussed. It is important to note that the charge transfer from the adsorbate to substrate increases the electric field near the metal surface for both incoming and scattered radiation which causes the SERS. Therefore, knowing the position of the charge transfer electronic transitions and their variation with sublayer is very important for generating the SERS spectra in these kind of nanostructures. A brief investigation on the main electronic configuration of the calculated electronic transitions of CYT/Au and CYT/Au/Ag complexes showed that the HOMO and HOMO-1 of the CYT contributed to the charge transfer from the CYT to nanosurface upon electron excitation. The HOMO-9 and HOMO-24 of the CYT/Au complex are corresponding to the HOMO and HOMO-1 of the CYT, respectively (see Figure 7). The shape of the electron density localized on the CYT in the HOMO-9 and HOMO-24 of the CYT/Au complex is the same as the electron density of HOMO and HOMO-1 of isolated CYT. Similarly, the HOMO-10 and HOMO-18 of the CYT/Au/Ag are corresponding to the HOMO and HOMO-1 of isolated CYT, respectively. Figure 7 shows the molecular orbitals of the CYT/Au contributing to the charge transfer electronic transitions. As can be seen, there are four electronic transitions located at 658.95 (HOMO-9 → LUMO+3), 728.07 (HOMO-9 → LUMO+2), 793.32 (HOMO-9 →LUMO+1) and 865.92 nm (HOMO-9 →LUMO) in the calculated absorption spectrum of CYT/Au containing the charge transfer from the HOMO of CYT to Au nanosurface. The electronic transitions containing the charge transfer from the HOMO-1 of the CYT to surface are located at 596.52 (HOMO-24 →LUMO+1), 596.26 (HOMO-24 →LUMO+1), 594.69 (HOMO-24 →LUMO+1), 636.90 (HOMO-24 →LUMO) and 636.14 nm (HOMO-24 →LUMO). The percentage of the charge transfer in each electronic transitions has also been identified in Figure 7. It is seen that the



electronic transitions located at 728.07 and 865.92 nm are mainly related to the charge transfer from the CYT to Au nanosurface with the percentage of 92 and 89%, respectively. The presence of Ag sublayer causes that the electronic transitions containing the charge transfers to move to the shorter wavelength. In addition, the number of electronic transitions, containing the charge transfer from the HOMO-1 of CYT to the LUMO and LUMO+1 of the nanosurface decreases in the CYT/Au/Ag compared to CYT/Ag complex. A brief investigation on the main electronic configuration of the calculated electronic transitions of the CYT/Ag and CYT/Ag/Au complexes showed that only the HOMO of the CYT contributed to the charge transfer from the CYT to nanosurface upon electron excitation. In the CYT/Ag complex, the HOMO-13 of the complex has contribution from the HOMO of CYT. Two molecular orbitals of CYT/Ag/Au complex including HOMO-20 and HOMO-21 have contribution from the HOMO of CYT. Figure 8 shows that there are four transitions with the main electronic configurations containing the charge transfer from the HOMO of CYT (HOMO-13 of CYT/Ag) to the Ag nanosurface. The wavelength of each transition and its charge transfer percentage have also been reported in Figure 8. The presence of Au sublayer caused the number of charge transfer electronic transitions to decrease in the CYT/Ag/Au complex compared to CYT/Ag complex but the percentage of charge transfer of each transition to increase. Comparison of Figure 8 with 7 shows that the charge transfer from the CYT to nanosurface take places from the HOMO and HOMO-1 of CYT in the CYT/Au and CYT/Au/Ag complexes while in the CYT/Ag and CYT/Ag/Au the charge transfer is only from the HOMO of CYT to nanosurface.


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LUMO+3 LUMO+3

LUMO+2

LUMO+2 HOMO-9 HOMO-10

LUMO+1

LUMO+1

LUMO LUMO

LUMO+1

HOMO-24

LUMO+1

HOMO-18

LUMO

LUMO

CYT/Au/Ag

CYT/Au

Figure 7. The molecular orbitals of the CYT/Au and CYT/Au/Ag complexes contributing in the charge transfer from the CYT to nanosurface during electron excitation. The wavelength and percentage of charge transfer for each electronic transitions have been identified. The HOMO-9 and HOMO-24 of the CYT/Au complex are corresponding to the HOMO and HOMO-1 of the isolated CYT. Similarly, the HOMO-10 and HOMO-18 of the CYT/Au/Ag complex are corresponding to HOMO and HOMO-1 of isolated CYT.



LUMO+1

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HOMO-20

HOMO-13

LUMO

LUMO

CYT/Ag

HOMO-21

CYT/Ag/Au

Figure 8. The molecular orbitals of the CYT/Ag and CYT/Ag/Au complexes contributing in the charge transfer from the CYT to nanosurface during electron excitation. The wavelength and percentage of charge transfer for each electronic transitions have been identified. The HOMO-13 of the CYT/Au complex is corresponding to the HOMO of the isolated CYT. Two molecular orbitals of the CYT/Au/Ag complex including HOMO-20 and HOMO-21 have contribution from the HOMO of isolated CYT. (d) Comparison of IR spectra Most of the vibrational spectroscopic studies related to the adsorption of DNA bases on metal nanostructures are often related to the SERS and not IR spectroscopy. Ataka and Osawa have studied the adsorption of CYT on a gold electrode at different potentials and recorded the IR spectrum of CYT at different electrode potentials to obtain information about the adsorption geometry of the CYT on the electrode surface.60 Figure 9a compares the calculated IR spectrum of CYT in the CYT/Au complex with that in the CYT/Au/Ag complex to see the effect of Ag sublayer on the IR spectrum of CYT. The presence of Ag as a sublayer in the CYT/Au/Ag complex causes considerable changes in the IR spectrum of CYT compared to that in the CYT/Au complex in the range of 500 to 1000 cm-1. The peak of highest intensity in the IR spectrum of CYT/Au


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complex is peak No.1 located at 513.224 cm-1 related to the wagging of one of the H atoms of NH2 group (see Figure 10a). In the IR spectrum of CYT/Au/Ag complex, this peak shifts to the lower wavenumber (476.759 cm-1) and the wagging of two H atoms of NH2 group takes place in the vibrational mode of this peak. The other important change in the IR spectrum of CYT due to Ag sublayer is the increase of the energy gap between peaks No. 2 and 3 in the IR spectrum of CYT/Au/Ag complex compared to the CYT/Au complex. The peaks No. 2 and 3 in the IR spectrum of CYT/Au complex are mainly related to the wagging of one of the H atoms of NH2 group, wagging of the N-H and C-H of CYT ring. The presence of Ag sublayer causes the wagging of the second H atom of NH2 group of CYT to become active in the CYT/Au/Ag complex. It can be concluded that the Ag sublayer activates the wagging of both H atoms of the NH2 group of the CYT related to peaks No. 1, 2 and 3. The other important change in the IR spectrum of CYT due to the Ag sublayer is seen in the range of 3000 to 4000 cm-1. The Ag sublayer shifts the vibrational peak, related to the N-H stretching of the NH group of CYT ring in the plane of the molecule, to the higher wavenumber. Figure 9b compares the IR spectrum of CYT in the CYT/Ag complex with that in the CYT/Ag/Au complex. The peak No.1 (437.051 cm-1) in the IR spectrum of CYT/Ag complex is mainly related to the wagging of one of the H atoms of the NH2 group from the plane of the molecule (see Figure 10b). The presence of Au sublayer shifts this peak to a higher wavenumber (467.349 cm-1) in the spectrum of the CYT/Au/Ag complex. Two vibrational bands with relatively similar intensities are seen in the IR spectrum of the CYT/Ag/Au system in the range of 500 to 600 cm-1 (peaks No. 2 and 3 in Figure 9b). The peak No.2 is related to the wagging of H atoms of the NH2 group from the plane of the molecule so that the displacement of one of the H atoms is greater than the other. Peak No.3 is related to the wagging of one of the H atoms of the NH2 group



and N-H group of the ring, simultaneously. The important difference between the IR spectrum of CYT/Ag and CYT/Ag/Au is related to the region of 500 and 600 cm-1. The Au sublayer causes the intensity of peak No.2 in the spectrum of the CYT/Ag complex to increase considerably in the spectrum of CYT/Ag/Au without any energy shift. Also, Peak No.3 in the spectrum of CYT/Ag shifts to the lower wavelength and its intensity decreases in the spectrum of CYT/Ag/Au complex. Peak No.4 in the IR spectrum of CYT/Ag/Au complex is only related to the wagging of N-H of the ring. The Au sublayer shifts this peak to the lower wavelength in the spectrum of the CYT/Ag/Au complex. Peak No. 5 in the spectrum of CYT/Ag and CYT/Ag/Au complexes is mainly related to the N-H stretching of NH2 group of CYT and Au sublayer shifts this peak to higher wavelength and decreases its intensity.


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1400

(a)

Intensity (arb.uni)

40

1

CYT/AuAu CYT/Au/Ag Ag-Au

1200 1000

30

800 20

1

600

4

3 2

400

4

10

200

2

3

0

0 4000 3800 3600 3400 3200 3000

2000

1500

1000

500

0

Wavenumber (cm-1) 50

1

5

(b) Intensity (arb.uni)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


CYT/Ag Ag CYT/Ag/Au Au-Ag

500

40

3 4

1

4

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5

400 300

20

2 3

200

10

100

0

0

2

4000 3800 3600 3400 3200 3000

2000

1500

1000

500

Wavenumber (cm-1)

Figure 9. (a) The calculated IR spectrum of CYT on the Au (blue spectrum) and Au/Ag nanosurfaces (red spectrum). (b) The calculated IR spectrum of CYT on Ag (blue spectrum) and Ag/Au nanosurfaces (red spectrum). Comparison of intensity and position of the vibrational bands with the same numbering shows the difference between the IR spectra due to the sublayer.


0


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CYT/Au/Ag (3)

(4)

(1)

(2)

CYT/Au (3)

(4)

(1)

(2) (a)

CYT/Ag/Au (5)

(4)

(3)

(5)

(4)

(3)

(2)

(1)

CYT/Ag (2)

(1)

(b)

Figure 10. (a) The vibrational modes of the peak numbered in the IR spectrum of CYT/Au and CYT/Au/Ag in Figure 9a. (b) The vibrational modes of the peak numbered in the IR spectrum of CYT/Ag and CYT/Ag/Au in Figure 9b. The white, gray, blue and red balls show the H, C, N and O atoms, respectively.


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(e) Comparison of Raman spectra In this part, the normal Raman and the SERS spectra of CYT adsorbed on the selected nanosurfaces are calculated and analyzed. The SERS spectra were calculated using the TD-DFT method in the infinite lifetime approximation at the wavelengths near the absorption lines corresponding to the charge transfer from the CYT to nanosurfaces. Although, within the infinite lifetime approximation, the actual changes in the intensity of each vibrational band cannot be estimated, the relative intensities of vibrational bands are accurate and comparable with the relative intensities of vibrational bands in the SERS spectra79 calculated using the finite lifetime damping. It is important to note that three effects including (a) the surface plasmon resonance (SPR), (b) photo-induced charge transfer (CT), and (c) molecular resonance (MR) are responsible for the intensity enhancement of vibrational bands in the SERS spectrum. It is very difficult to separate the contribution of each mechanism by purely experimental means and consequently, the quantum chemical calculations are necessary. Although, there are several papers in the literature51-76 on the SERS of DNA bases adsorbed on different metal nanostructures, especially, Ag, Au, and their bimetallic nanostructures, the charge transfer enhancement contribution in the SERS has not been studied for the DNA bases on metal surfaces. It is important to note that the absorption lines that are appropriate for our calculations are those with no other absorption lines near them. It is possible to easily pick a wavelength higher or lower than the target wavelength. In this case, the pure effect of charge transfer on the Raman spectra of CYT on the selected nanosurfaces and the vibrational modes showing intensity enhancement due to the charge transfer can be determined. To the authors, knowledge, there is no experimental and theoretical study on the SERS spectra of CYT on these surfaces due only to the charge transfer from the CYT to nanosurface.



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The vibrational modes of CYT showing intensity enhancement in the SERS spectra are determined for each nanosurface. As mentioned, there were some absorption lines in the UV spectra of CYT/Ag, CYT/Ag/Au, CYT/Au and CYT/Au/Ag complexes related to the charge transfer from the CYT to nanosurface (see Figures 7 and 8). The absorption lines located at 865.92 and 728.07 nm are appropriate for calculating the SERS spectra of CYT/Au structure because there is no other absorption line near them and the intensity enhancement is mainly due to the charge transfer from the CYT to nanosurface. Therefore, the SERS spectra of the CYT/Au structure were calculated at two wavelengths including 873.92 and 725.925 nm, separately. The selected wavelength for the CYT/Au/Ag structure was 713.51 nm. The SERS spectra of the CYT/Ag were calculated at two different wavelengths including 496.50 and 494.585 nm. Only one SERS was calculated for CYT/Ag/Au system at a wavelength of 502.77 nm. To obtain the intensity of each vibrational band in the SERS spectrum, the calculation of the Raman activity (Sj) of the related vibrational mode is necessary. For this purpose, the TD-DFT method was used for the calculation of the Sj of each vibrational mode at each selected wavelength. The calculated value of Sj for each vibrational mode was used in the following relationship to calculate the Raman intensity.51

∂σ𝑗∂Ω=24π445ν0−ν𝑗41−𝑒−ℎ𝑐ν𝑗𝑘𝑇ℎ8π2𝑐ν𝑗𝑆𝑗 (1)

𝑆𝑗=45𝑑𝛼𝑑𝑄𝑗2+7𝑑γ𝑑𝑄𝑗2

(2)

where σ is the Raman cross-section, Ω is the depolarization ratio, νo is the frequency of the incident light which is corresponding to the wavelength selected from the absorption spectrum, νj is the frequency of the vibrational mode, c is the velocity of light, α is the polarizability, γ is the anisotropic polarizability, and Qj is the normal coordinate. The normal Raman spectra were


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calculated using the normal Frequency calculations in G09 package considering static electric dipole approximation. Figures 11a and 11b demonstrate the SERS of CYT/Au complex, calculated at 725.925 and 873.92 nm, respectively (black spectra) and compare them with the calculated normal Raman spectrum of CYT/Au complex (blue spectra). As seen in Figure 11b, the intensity enhancement is seen for four vibrational bands located in the range of 1300 to 1800 cm-1 (1356.17, 1489.17, 1638.95 and 1686.88 cm-1) at 873.92 nm. These vibrational bands have been numbered in Figure 11a (peaks No.1 to 4). When the wavelength shift to 725.925 nm, the enhancement of intensity is seen only for two vibrational bands located at 1356.17 and 1489.17 cm-1 (peak No.1 and 2). It is important to note that the wavelength of 873.92 nm is near the 865.92 nm which corresponds to electron excitation from HOMO-9 to LUMO while the wavelength of 725.925 nm is near the 728.07 nm which is corresponding to the electron excitation from HOMO-9 to LUMO+2. The vibrational modes related to the vibrational bands numbered in Figure 11b for CYT/Au have been shown in Figure 12. Figure 11c compares the SERS spectrum of CYT/Au/Ag system calculated at 713.51 nm with its normal Raman spectrum. As seen, the enhancement of intensity is seen for three vibrational bands which have been numbered in the spectrum. Peak No. 1, 2 and 3 have been located at 1354.26, 1489.25 and 1635.33 cm-1, respectively, and their vibrational modes have been shown in Figure 12. Comparison of Figure 11c with 11a and 11b shows that the presence of Ag sublayer caused the Raman shift of peaks No.1, 2 and 3 to move slightly to the lower wavenumber. Figure 11 shows that peak No.1 and 2 in the Raman spectra of the CYT/Au and CYT/Au/Ag complexes show more sensitivity for intensity enhancement due to the charge transfer from the CYT to the nanosurfaces compared to the other vibrational bands. Therefore, peak No.1 and 2 could be selected as reference vibrational bands for the charge transfer effect. The other important



point is that the displacement of the atoms in the vibrational mode related to peak No.2 changes in the CYT/Au/Ag complex compared to the CYT/Au complex so that the stretching of the C-N bond of the ring of CYT is added to the vibrational mode of this peak in the CYT/Au/Ag complex.


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2 CYT/Au/Ag

λ=713.51 nm

1 3

(c)

2000

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1400 2

CYT/Au

4

1200

1000

1

800

600

λ=873.92 nm

3

(b)

2000

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600

2

CYT/Au

λ=725.92 nm 1

(a)

2000

1800

1600

1400

1200

1000

800

600

-1

Raman Shift (cm )

Figure 11. Comparison of the calculated SERS spectra of CYT (black spectrum) (a) at 725.92 nm for CYT/Au (b) at 873.92 nm for CYT/Au and (c) at 713.51 nm for CYT/Au/Ag. The blue spectrum in (a) and (b) are the same and it is the normal Raman spectrum of CYT in CYT/Au. The blue spectrum in (c) is the normal Raman spectrum of CYT in CYT/Au/Ag.



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CYT/Au 873.92 nm

(1)

(2)

(3)

(2)

(3)

(4)

CYT/Au/Ag

(1)

Figure 12. The vibrational modes related to the vibrational bands showing intensity enhancement numbered in Figure 11b and 11c for CYT/Au and CYT/Au/Ag, respectively. Figures 13a and 13b compare the calculated SERS spectrum of CYT/Ag calculated at the wavelengths of 494.59 and 496.50 nm, respectively. It is seen that the change of wavelength from 494.59 to 496.50 nm creates considerable changes in the intensity enhancement of vibrational bands. When the selected wavelength is 494.59 nm, the enhancement of the vibrational bands takes place in the range of 600 to 800 cm-1 and 1400 to 1800 cm-1. The enhancement of the vibrational bands occurs in the range of 1400 to 1800 cm-1 at 496.50 nm. The vibrational bands in the Raman spectrum of CYT/Ag system showing considerable intensity enhancement have been numbered in Figure 13a and 13b. These vibrational bands in Figure 13a have been located at 625.14, 778.887, 1633.47 and 1675.38 cm-1 and their related vibrational modes have been shown in Figure 14. The vibrational bands numbered in the Raman spectrum of CYT/Ag calculated at 496.50 nm are at 1558.06 and 1680.39 cm-1. Based on Figures 13a and 13b, the vibrational bands located in the range of 1550 to 1700 cm-1 are good candidates for the SERS effect due to the charge transfer from


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the CYT to Ag nanosurface. In the presence of Au sublayer, there are two absorption lines mainly related to the charge transfer from the CYT to surface located at 503.35 and 509.76 nm. The absorption line located at 503.35 nm is appropriate for calculating the SERS spectrum because of the absence of absorption lines related to the excitation of the surface near it. Figure 13c compares the SERS spectrum of CYT/Ag/Au calculated at 502.77 nm. It is seen that the enhancement of intensity takes place mainly for two vibrational bands located at 617.244 (peak No.1) and 944.339 (peak No.2) cm-1. The vibrational mode of peak No.1 is related to the out of plane bending of NH of the ring and the vibrational mode of the second peak is related to the out of plane bending of C-H bonds of the ring.



Page 38 of 106

λ=502.77 nm

CYT/Ag/Au 2

1

(c)

2000

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1

CYT/Ag

800

600

λ=496.50 nm

2 (b)

2000

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CYT/Ag

1600

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3

800

2

600

λ=494.59 nm 1

(a)

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Raman Shift (cm-1)

Figure 13. Comparison of the calculated SERS spectra of CYT (black spectrum) (a) at 494.59 nm for CYT/Ag (b) at 496.50 nm for CYT/Ag and (c) at 502.77 nm for CYT/Ag/Au. The blue spectrum in (a) and (b) are the same and it is the normal Raman spectrum of CYT in CYT/Ag. The blue spectrum in (c) is the normal Raman spectrum of CYT in CYT/Ag/Au.


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⊕

CYT/Ag 494.59 nm

(1)

(2)

(3)

(4)

CYT/Ag 496.50 nm

(2)

(1) CYT/Ag/Au

(1)

(2)

Figure 14. The vibrational modes related to the vibrational bands showing intensity enhancement numbered in Figure 13 for CYT/Ag and CYT/Ag/Au.

Conclusion The experimental UV absorption spectra of different nanostructures composed of Au and Ag metals, especially in the form of pure and bimetallic core-shell nanoparticles, have been reported in literature and the change in the maximum position and intensity of their absorption spectra with the percentage of Ag and Au in the core-shell nanoparticles have been demonstrated, without any theoretical reasons for the changes. Therefore, in the first part of this work, the pure and bimetallic nanosurfaces of Ag and Au metals were used as a model to interpret the experimental results. The theoretical results showed that the presence of Au sublayers in the



Ag/Au nanosurface increases the intensity of absorption spectrum considerably and shifts the maximum of absorption spectrum to higher wavelength compared to Ag nanosurface. In the case of Au/Ag nanosurface, the Ag sublayer increases the intensity of absorption spectrum and shifts it to the lower wavelength compared to Au nanosurface. The calculations showed that the presence of sublayer in nanosurface increases the number of allowed electronic transitions compared to pure nanosurface which is accompanied with the increase in the intensity of absorption spectrum. To interpret the variations observed in the absorption spectra due to the sublayer, the TDOS of the bimetallic nanosurfaces were calculated and compared with the DOS of pure nanosurfaces. Comparing of the TDOS of Ag/Au nanosurface with that of pure Ag nanosurface showed a decrease in the intensity of the TDOS of Ag/Au nanosurface in the energy region related to the occupied states along with a small shift to more negative energy. Also, it was observed that the Au sublayer did not nearly have effect on the TDOS of unoccupied states in the region of -2.5 to 7.5 eV which meant that the number of unoccupied states in this energy region were nearly constant. Based on these comparisons, it was concluded that the main reason for the increase of intensity and shift of the maximum of absorption spectrum of Ag/Au nanosurface to higher wavelength is the allowance of many electronic transitions which were forbidden in the Ag nanosurface. Comparison of the TDOS of Au/Ag nanosurface with that of Au nanosurface showed that the intensity of peak of TDOS related to the occupied states of Au/Ag increased compared to pure Au surface and shifts to more negative energy which this energy shift was considerably more than that observed for the Ag/Au nanosurface compared to Ag nanosurface. This increase showed that the occupied states of the Au/Ag nanosurface became closer to each other compared to Au nanosurface due to the Ag sublayer. Similar to the Ag/Au nanosurface, the presence of Ag sublayer in the Au/Ag nanosurface did not change the number of unoccupied states of nanosurface in the


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energy range of -2.5 to 7.5 eV because of the small changes in the TDOS of the nanosurface compared to pure Au nanosurface. The shift of the absorption spectrum of the Au/Ag nanosurface compared to Ag nanosurface was attributed to the increase of the energy separation between the occupied and unoccupied states. The interaction of the CYT with the nanosurfaces shifted their absorption spectra to the higher wavelength compared to clean nanosurfaces. The presence of the CYT in the CYT/Ag/Au complex increased the intensity of its absorption spectrum compared to clean Ag/Au nanosurface while the opposite trend was seen for the CYT/Au/Ag complex compared to Au/Ag nanosurface. It was found that the adsorption of CYT on the Ag/Au nanosurface increased and decreased the contribution of Au and Ag in the unoccupied states compared to clean Ag/Au nanosurface, respectively. In the CYT/Au/Ag, the presence of the CYT does not provide significant changes in the PDOS of Ag and Au compared to those of clean Au/Ag nanosurface. It was seen that the interaction of the CYT with nanosurfaces in the CYT/Au/Ag and CYT/Ag/Au complexes increased their TDOS in the energy region related to the unoccupied states. The decrease of the intensity of the maximum of absorption spectrum of the CYT/Au/Ag complex compared to Au/Ag nanosurface, in spite of the increase of the number of its allowed transitions, was attributed to the decrease of the oscillator strength of its electronic transitions. In the second part of this work, the effect of sublayer on the IR and Raman spectra of CYT was studied and the vibrational modes discriminating this effect were determined. Comparison of the IR spectra of CYT in the CYT/Au and CYT/Ag complexes with those in the CYT/Au/Ag and CYT/Ag/Au complexes, respectively, showed that the vibrational peaks sensitive to the sublayer have been located in the range of 400 to 1000 cm-1 and mainly related to the wagging of the hydrogen atoms of NH2 group, C-H and N-H of the ring. The other region in the IR spectrum



which reflects the effect of sublayer is the region of 3400 to 3800 cm-1. The Ag sublayer in the CYT/Au/Ag complex causes the peak related to the stretching of N-H to moves to a higher wavenumber. In the presence of Au sublayer in the CYT/Au/Ag complex, the vibrational mode related to the symmetry stretching of the NH2 group moved to a lower wavenumber. The charge transfer SERS spectra of the CYT when adsorbed on the selected nanosurfaces were also calculated. The selected excitation wavelengths for calculating the SERS spectra were close to the wavelength related to the charge transfer from the CYT to nanosurface. The vibrational modes of the CYT represented by Raman peaks allowed the intensity enhancement due to the charge transfer to be determined for each nanosurface. It was observed that for the CYT/Au and CYT/Au/Ag complex, the peaks showing enhancement intensity have been located in the range of 1300 to 1800 cm-1 and the Ag sublayer increased the enhancement intensity of some vibrational bands compared to what was observed for the CYT/Au complex in this region of wavenumber. The presence of Au sublayer in the CYT/Ag/Au complex changes the patterns the SERS spectrum of the CYT considerably compared to what was observed for CYT/Ag (enhancement occurring in the 600 to 1000 cm-1 region).


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Acknowledgement The authors thank to Isfahan university of technology (IUT) for its financial support. Also, the authors gratefully acknowledge the Sheikh Bahaei National High Performance Computing Center (SBNHPCC) for providing computing facilities and time.



Associated Contents Supporting Information Explanations about the preparation and optimization of the Au, Ag, Ag/Au and Au/Ag nanosurface and their complexes with CYT performed in our previous work (reference 40) Author information Corresponding Author *Tel: +98 31 33913243. Fax: +98 31 33912350. E-mail: [email protected] ; [email protected]

Notes The authors declare no competing financial interest.


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TOC Graphic

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A Theoretical Spectroscopic Study on the Au, Ag, Au/Ag, and Ag/Au Nanosurfaces and Their Cytosine/Nanosurface Complexes: UV, IR, and Charge Transfer SERS Spectra

Hossein Farrokhpour* and Maryam Ghandehari Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran

Corresponding Author: Hossein Farrokhpour E-Mail: [email protected]; [email protected]


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ABSTRACT The first part of this work is related to the calculation of the absorption spectra of pure Ag and Au nanosurfaces, bimetallic nanosurfaces composed of Ag and Au metals (Au/Ag and Ag/Au) and the nanosurfaces interacted with cytosine (CYT/Au, CYT/Au/Ag, CYT/Ag and CYT/Ag/Au). Comparison of the absorption spectra and changes in the total and partial density of states (TDOS and PDOS) of the systems allowed the effect of metallic structure of the sublayer and adsorbate on the intensity and position of the maximum of the spectra to be explored. The absorption lines responsible for the charge transfer from the CYT to nanosurfaces due to the electronic excitation for each CYT/nanosurface were determined and the effect of sublayer on these electronic transitions was studied. In the second part of this work, the effect of metallic structure of sublayer on the IR spectrum of the CYT adsorbed on the Au/Ag and Ag/Au nanosurfaces was studied and the vibrational bands of the CYT that were sensitive to the metallic structure of sublayer were determined. In addition, the frequency-dependent Raman spectra of the CYT adsorbed on the selected nanosurfaces were calculated at several wavelengths corresponding to electronic excitation charge transfer from the CYT to the nanosurface. The vibrational bands of the CYT showing the intensity enhancement due to the charge transfer in the Raman spectrum for each nanosurface were determined. The theoretical spectroscopic results presented in this work are very useful for the interpretation of experimental results especially when the CYT is adsorbed on nanosurfaces such as Ag, Au and their bimetallic nanosurfaces.



Introduction Metal nanostructures in the form of nanoparticles, nanosurfaces, and nanoclusters, especially those composed of Au and Ag, are the most common candidates in biology and biomedical applications for designing of nanosensors and drug delivery nanocarrier systems. 1 The reason for using Ag and Au metals for constructing nanostructures compared to other metals is due to their localized surface plasmon resonance (LSPR), which are located in the visible region and near infrared region2,3, and their biocompatibility properties.4 Also, Ag and Au metals are the most intensively investigated surface-enhanced Raman scattering (SERS) metals. 5-15Besides much attention to pure Au and Ag nanostructures, there is much interest to bimetallic nanostructures (core-shell and alloy structures) composed of Ag and Au16-27 due to their much higher LSPR intensity compared to pure Au nanostructures and their greater chemical stability compared to pure Ag nanostructures.16 Also, the electrical, optical and catalytic properties of the bimetallic nanoparticles composed of Au and Ag are strongly dependent on the composition and arrangement of metal atoms. Three kinds of bimetallic nanoparticles composed of Ag and Au have been synthesized including AgcoreAushell, AucoreAgshell and alloyed AgAu. 19-21,23 Among the biological molecules, the interaction of DNA with metal nanostructures constructed from noble metals (Au, Ag and Cu) is the subjects of great interest in various fields such as biotechnology and nanotechnology. 28-38 To explore the mechanism of interaction of DNA with metal nanostructures, the study of the adsorption of isolated DNA bases on metal nanostructures is a promising approach. This is because the knowledge about the fundamental modes of metal interaction with a simple DNA base would greatly enhance our understanding of how metals interact with more complex nucleic acid structures such as DNA. There are different experimental and theoretical papers in literature related to the interaction of isolated DNA bases


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with nanostructures including nanoparticles, nanosurfaces, and nanoclusters of noble metals and their bimetallic nanostructures.39-50 In the experimental papers, different spectroscopic techniques including UV, IR, and SERS have been used to study the adsorption of DNA bases on the nanostructures. The displacement of the position of LSPR of metal nanostructure in the UV spectrum due to the interaction between nanostructure and adsorbate and change in its intensity have been used as a tool for sensing of DNA bases with nanostructures. The IR and SERS spectra have been employed to obtain information about the adsorption geometry of DNA bases on the surface of nanostructures.51-76 In continuation of our previous work,40 two aims are followed in this paper. (i) The absorption spectra of bare Au, Ag, Au/Ag, and Ag/Au nanosurfaces were calculated and compared with each other to see the effect of sublayer on the absorption spectra. Although there are published papers in literature on the synthesis of pure and bimetallic nanostructures of these metals and their characterizations based on the variations in their absorption spectra, the theoretical studies to interpret these variations are very limited. In this work, theoretical calculations were conducted to interpret and explain these variations. (ii) Although the adsorption of DNA bases on metal nanosurfaces and nanoparticles have been studied theoretically in literature, these studies mainly focused on the calculation of adsorption energy, adsorption geometry, charge transfer and mixing of molecular orbitals of metal nanostructure with those bases. In addition, theoretical studies of their absorption, IR and Raman spectra is very limited. In our previous work, 40 the adsorption of cytosine (CYT) on pure Ag and Au nanosurfaces (CYT/Ag and CYT/Au), and Ag/Au and Au/Ag bimetallic nanosurfaces (CYT/Ag/Au and CYT/Au/Ag) were studied and the effect of sublayer on the adsorption of CYT on these nanosurfaces was investigated. In this work, the absorption spectra of these systems along with the IR and SERS spectra of CYT adsorbed on the nanosurfaces were



calculated and compared with each other to see how the metallic structure of sublayer changes these spectra. The SERS spectra of the CYT were calculated at wavelengths corresponding to the charge transfer (electron transfer) from the CYT to nanosurface due to the electronic excitation. The vibrational modes of the CYT showing intensity enhancement in the calculated SERS spectra were determined. It is important to note that this is the first theoretical report on the SERS spectra of the CYT adsorbed on metal nanostructure due to only charge transfer from it to the substrate.

Computational details The initial structures of bare nanosurfaces and CYT/nanosurface complexes of this work were constructed by reducing the size of their corresponding optimized structures reported in our previous study.40 The detailed information about the construction and optimization of clean nanosurfaces and CYT/nanosurface structures have been given in our previous paper [40] (see section 2 and Figure 1, S1 and S2 in reference 40). However, some brief explanations have been given in supporting information. The size of the optimized nanosurfaces and CYT/nanosurface complexes in our previous work40 were so big for calculating the UV, IR and SERS spectra, that these calculations were nearly impossible. Therefore, reducing the size of the nanosurfaces was proposed. Figure 1a shows the structure of CYT/Au/Ag complex taken from reference 40. The size of the optimized structures reported in reference 40 was reduced so that the number of metal atoms decreased from 224 to 76 atoms. It is important to note that, the size reducing was performed without any change in the position and orientation of the CYT on the nanosurfaces. To check the validity of the reduced CYT/nanosurface structures with respect to the location of their local minima on the potential energy surface, frequency calculation was performed for each reduced CYT/nanosurface using the method of optimization in our previous work 40 (see supporting


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information). No imaginary vibrational frequencies were observed which meant that the reduced structures were still at the minimum of the potential energy surface of the new structures. Further optimization was performed on the reduced CYT/nanosurface structures in the form of a small deviation of the orientation of the CYT from its optimized orientation in the unreduced CYT/nanosurfaces in our previous work40. In this optimization all of the metal atoms of the reduced nanosurface were rigid except for the metal atoms of the first layer. After optimization, it was observed that the orientation of the CYT in the reduced CYT/nanosurface structures was nearly same as those obtained in our previous work40. Therefore, it was concluded that the reduced CYT/nanosurface systems can be considered an alternative candidate to the big structures reported in our previous work40. Figure 1b shows the optimized structure of the reduced CYT/Au/Ag structure from three different views. For more information about the theoretical method used for the optimization see supporting information. The absorption spectra of the reduced clean nanosurfaces and CYT/nanosurface structures were calculated by the time-dependent density functional theory (TD-DFT) method in the twolayer “our own n-layered integrated molecular orbital and molecular mechanics” (ONIOM) scheme considering 150 excited states in the calculation employing M06-L functional 78. The 6311++G(d, p) and LANL2DZ basis sets were used for the CYT and metal atoms in the quantum mechanics (QM) region, respectively, and the metal atoms in molecular mechanics (MM) region were described using universal force field (UFF) (see Figure 1). The IR and normal Raman spectra (static Raman spectra) of the CYT/nanosurface were calculated at the same level of theory using DFT method. Also, the frequency-dependent near resonance Raman (FDNRR) spectra of CYT were calculated at the wavelengths near the resonance of the electronic excitations corresponding to the charge transfer from the CYT to surface using the infinite-lifetime approximation employing



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TD-DFT method. In the FDNRR spectrum, the relative intensities of vibrational bands were the same as the SERS spectrum recorded at a wavelength equal to the resonance of the electronic excitation.79 Therefore, all of the FDNRR spectra calculated in this work are called SERS spectra throughout this paper. All of the calculations were performed using Gaussian 09 (G09) quantum chemistry package.80 The plots of total and partial density of states (TDOS and PDOS, respectively) were calculated using Multiwfn 3.4 software.81

(b)

(a)

Figure 1. (a) The optimized structure of the CYT/Au/Ag complex taken from reference 40. (b) The optimized reduced structure of the CYT/Au/Ag complex from three views. The yellow and blue colors show the Au and Ag metal atoms, respectively. The balls and dots show the atoms in the QM and MM regions, respectively, in the ONIOM scheme.


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Results and discussion (a) Absorption spectra of clean nanosurfaces There are several experimental papers in the literature on the synthesis of nanostructures composed of Au and Ag metals. Fan et al. synthesized pure Ag and Au nanoparticles and their alloys with the size of 3-5 nm.82 They observed that as the percentage of Ag increased in the bimetallic alloy nanoparticle the maximum of absorption spectrum shifted from 530 nm for pure Au to 400 nm for pure Ag and the composition of the alloy bimetallic nanoparticles was monitored through the absorption spectroscopy. Mott et al. synthesized pure Ag nanoparticles and coated them with a layer of Au with the average size of 20 nm.19 They found that as the thickness of Au layer increased the intensity of the absorption spectrum decreased and shifted to the higher wavelength. Adhyapak et al. synthesized pure Ag and Au nanoparticles and their bimetallic forms including AgAu alloy, AgcoreAushell, and AucoreAgshell nanoparticles and compared their absorption spectra with each other.83 Shmarakov et al. compared the antitumor activity of Au, Ag, Au coreAgshell and AgcoreAushell nanoparticles.84 They observed that the presence of Au as core shifted the absorption spectrum of AucoreAgshell to higher wavelength compared to pure Ag nanoparticles while the reverse trend was seen for AgcoreAushell nanoparticles compared to Au nanoparticles. Hu et al. synthesized Ag-Au bimetallic nanoparticles in the forms of alloy and core-shell and recorded their time-dependent absorption spectra.27 In addition, they used discrete dipole approximation to simulate the absorption spectra of structures based on the Mie theory.85 Their simulations showed that as the percentage of Ag as shell increased, the intensity of absorption spectrum increased and shifted to the lower wavelength. Li et al.21 synthesized three types of bimetallic nanoparticles including AgcoreAushell, AucoreAgshell and alloyed AgAu with the mean size of 4-5 nm and recorded their absorption spectra at different mole ratio of Ag and Au in the nanoparticle. They showed that the



presence of Au metal as the core in the AucoreAgshell nanoparticle with 1:1 mole ratio caused the maximum of its absorption spectrum (505.00 nm) to be located at a higher wavelength compared to pure Ag nanoparticles (460.00 nm). Kuladeep et al.23 synthesized the Au-Ag alloy nanoparticles with laser ablation and followed the variation in the absorption spectrum of nanoparticle while changing the percentage of Au and Ag in the metal nanoparticle. Samal et al. 86 proposed a simple and efficient methodology for the size-tunable synthesis of Au coreAgshell nanoparticles and recorded their absorption spectra along with the calculation of the absorption spectra using Mie theory. The calculated absorption spectra of clean nanosurfaces including (Ag and Ag/Au) and (Au and Au/Ag) have been demonstrated in Figures 2 and 3, respectively. As can be seen in Figure 2, the presence of Au sublayers in the Ag/Au nanosurface increases the intensity of absorption spectrum considerably, and shifts the spectrum to higher wavelength compared to the Ag nanosurface. The calculated position of the maximum of the absorption spectrum of Ag and Ag/Au nanosurfaces are 492.26 and 526.03 nm, respectively, which shows that the Au sublayers shift the absorption spectrum 33.7 nm to a higher wavelength. It is important to note that the shift of the position of the maximum absorption spectrum of Ag/Au nanosurface compared to pure Ag nanosurface is similar to what has been observed, experimentally, for Au coreAgshell nanoparticles compared to pure Ag nanoparticles of the same size.21 The position of the maximum of absorption spectrum of Ag and Ag/Au nanosurfaces from the current study is approximately 32 and 21 nm higher in wavelength, respectively, compared to the absorption spectrum of Ag and Au coreAgshell nanoparticles reported by Li et al.21 In Figure 3, the presence of Ag metal as a sublayer in the Au/Ag nanosurface showed the reverse trend so that the maximum of the absorption spectrum of Au/Ag nanosurface shifted to a lower wavelength compared to Au nanosurface and its intensity increases. This behavior is in


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agreement with the comparison of the experimental absorption spectra of Au and Ag coreAushell (with 1:1 mole ratio) nanoparticles reported by Li et al.21 The calculated position of the maximum of absorption spectrum of pure Au and Au/Ag nanosurfaces are 614.43 and 511.65 nm, respectively, and the experimental values reported by Li et al. 21 for the Au and AgcoreAushell nanoparticles are 540.00 and 512.50 nm, respectively. For more confirmation, Shmarakov et al. 84 have recorded the absorption spectra of Ag, Au, Au coreAgshell, and AgcoreAushell nanoparticles. They showed that the presence of Au as core shifted the maximum of the absorption spectrum of AucoreAgshell nanoparticles to a higher wavelength compared to Ag nanoparticles while using Ag metal as a core in the AgcoreAushell nanoparticles shifted the maximum of absorption spectrum to a lower wavelength. Although, the absorption spectra of the Ag, Au, Au coreAgshell, and AgcoreAushell nanoparticles have not been calculated in the current study, the trend in absorption spectra of the nanosurface with metalic sublayer calculated in this study are in agreement with their corresponding experimental pure and core-shell nanoparticles in the litrature. similar to what has been observed for the corresponding nanoparticles, experimentally in literature. The other important point is that the position of the LSPR for a metal nanostructure depends considerably on its shape, size, the environment of the nanostructure. Therefore, it should not be expected that the calculated LSPR positions would exactly match the values of their corresponding nanoparticles. The insets of Figures 2 and 3 show the oscillator strengths of the electronic transitions versus wavelength for the absorption spectra. It is seen that the presence of Au sublayer in the Ag/Au nanosurface increases the number of allowed electronic transitions compared to the Ag nanosurface, especially in the range of 480 to 560 nm. This increase caused the shift of the maximum of the absorption spectrum of Ag/Au nanosurface to higher wavelength compared to the Ag nanosurface. Similarly, the inset of Figure 3 shows that the presence of Ag sublayer in the



Au/Ag nanosurface increases the allowed electronic transitions in the range of 500 to 600 nm compared to Au. It can be concluded that the allowed transitions shift to the lower wavelength in the Au/Ag nanosurface compared to the Au nanosurface showing that the separation between the occupied and unoccupied states has been increased in Au/Ag nanosurface. Comparison of the inset of Figure 2 with that of Figure 3 shows that the increase in the number of allowed electronic transitions of a bimetallic nanosurface compared to its pure nanosurface for Ag/Au is considerably more than that for Au/Ag nanoaurface.


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CYT/Ag/Au Au_Ag_CY 25 CYT/Ag/Au

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20

Au_Ag Ag/Au

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CYT/Ag

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x10 (L/mol/cm)x10 Molar absorption coefficient

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


CYT/Ag

Ag

Ag_CY

0.00 500 600 700 800 900 1000

10

Wavelength (nm)

Ag 5

0 500

600

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Figure 2. The calculated UV absorption spectra of clean nanosurfaces including Ag (blue spectrum) and Ag/Au (black spectrum) along with the calculated UV spectra of the complexes of cytosine (CYT) with Ag (CYT/Ag ; red spectrum) and Ag/Au (CYT/Ag/Au ; green spectrum). The inset shows the oscillator strengths of the electronic transitions of each UV spectrum.



Au/Ag Ag_Au 0.35

30

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25 -3

CYT/Au/Ag Ag_Au_CY

20

Oscillator strength

0.25 Au/Ag

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Molar absorption coefficient x10 (L/mol/cm)x10

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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CYT/Au

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10

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CYT/Au Au_CY

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Figure 3. The calculated UV absorption spectra of clean nanosurfaces including Au (blue spectrum) and Au/Ag (black spectrum) along with the calculated UV spectra of the complexes of cytosine (CYT) with Au (CYT/Au ; red spectrum) and Au/Ag (CYT/Au/Ag ; green spectrum). The inset shows the oscillator strengths of the electronic transitions of each UV spectrum.


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Comparison of the TDOS and PDOS of the bimetallic nanosurfaces with pure ones provides useful information about the effect of sublayer on the occupied and unoccupied states. Figure 4a shows the calculated TDOS and PDOS of Ag/Au nanosurface and compares them with the TDOS of pure Ag nanosurface. It is seen that the TDOS of Ag nanosurface (green plot) shows a strong peak located at -8.11 eV related to the occupied molecular orbitals. The presence of Au sublayer in the Ag/Au nanosurface causes that the intensity of this peak to decrease (see the black curve in Figure 4a) considerably, and its position to slightly shift to a more negative energy (-0.33 eV). This intensity decrease shows that the energy separation between occupied orbitals has been increased in the Ag/Au compared to Ag nanosurface. On the other hand, the TDOS of Ag/Au nanosurface is nearly same as the DOS of Ag nanosurface in the range of -2.50 to 7.50 eV with the slight decrease in its intensity indicating that the number of unoccupied states has been slightly decreased in this energy region for Ag/Au nanosurface. Also, there is an increase in the number of the unoccupied states in the region between 7.50 and 20 eV for the Ag/Au nanosurface compared to Ag nanosurface while, a decrease is seen in the number of unoccupied states for the Ag/Au nanosurface compared to Ag nanosurface for the energies higher than 20 eV. Based on Figure 4a, the main effect of the Au sublayer is the decrease of the density of states of occupied states and shifting them to the lower energy. Based on the comparison of TDOS of Ag/Au nanosurface with that of Ag surface, it is expected that the maximum of absorption spectrum of Ag/Au should slightly shift to the lower wavelength while the reverse trend is seen in Figure 2. Therefore, it can be concluded that the main reason for the shift of the maximum of absorption spectrum of Ag/Au nanosurface to higher wavelength is the allowance of many electronic transitions which were forbidden for Ag nanosurface. It should be noted although the number of



Au atoms in the Ag/Au nanosurface is three times more than Ag atoms, the PDOS of Ag fragment (red curve in Figure 4a) is comparable with that of Au fragment (blue curve). The contribution of Au fragment in the occupied and unoccupied states of Ag/Au nanosurface is greater than Ag fragment. Figure 4b shows the calculated TDOS and PDOS of Au/Ag nanosurface and compare them with the DOS of pure Au nanosurfaces. It is seen that the contribution of Ag sublayers in the occupied molecular orbitals is considerably greater than the contribution of Au layer based on the comparison of the PDOS of Au (blue curve) and Ag fragments (red curve) in the range of -10 to 5 eV. Comparison of Figure 4b with 4a shows that the contribution of sublayer in the occupied molecular orbitals of the Au/Ag nanosurface is considerably greater than that in the Ag/Au nanosurface. Also, it is seen that the intensity of the peak of TDOS related to the occupied states of Au/Ag increases compared to pure Au surface and shifts to more negative energy (-0.79 eV) and its width decreases. This observation is opposite to what was observed for the TDOS of Au/Ag nanosurface compared to DOS of pure Ag nano surface. The increase of the intensity of TDOS of Au/Ag compared to Au in the range of -10 to -5 eV shows that the occupied states of the Au/Ag nanosurface become closer to each other compared to Au nanosurface. The TDOS of Au/Ag nanosurface, in the range of -2.5 to 7.5 eV related to the unoccupied states, increases slightly compared to Au nanosurface. Since, the occupied states of Au/Ag nanosurface shifts to more negative energies and the change in the DOS of its unoccupied states in the range of -2.5 to 7.5 eV is very small, it can be concluded that the energy separation between the occupied and unoccupied states increases in Au/Ag nanosurface and its absorption spectrum should shift to the lower wavelength compared to Au nanosurface which is in agreement with what has been shown in Figure 3.


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Density states (DOS) Density of of states (states/eV)

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Energy (eV) Figure 4. (a) The calculated total density of states (TDOS) of Ag and Ag/Au nanosurfaces along with the partial DOS (PDOS) of the Au and Ag fragments of the Ag/Au nanosurface. The solid and dashed lines show the energy position of the HOMO of Ag/Au and Ag nanosurfaces, respectively. (b) The calculated TDOS of Au and Au/Ag nanosurfaces along with the PDOS of



the Au and Ag fragments of the Au/Ag nanosurface. The solid and dashed lines show the energy position of the HOMO of Au/Ag and Au nanosurfaces, respectively. (b) Absorption spectra of CYT/Ag/Au, CYT/Au/Ag, CYT/Ag, and CYT/Au Figures 2 and 3 also showed the calculated absorption spectra of CYT+nanosurface complexes (CYT/Ag/Au, CYT/Ag, CYT/Au/Ag, and CYT/Au). It was seen that the presence of CYT on the nanosurfaces shifted their absorption spectra to higher wavelength. The presence of CYT on the Ag nanosurface shifted the maximum of its spectrum to higher wavelength approximately 13 nm compared to the spectrum of clean Ag nanosurface. The corresponding shift for the CYT/Ag/Au complex was approximately 9 nm compared to clean Ag/Au nanosurface. It can be seen that the presence of Au as a sublayer decreased this wavelength shift. The magnitude of this shift for the CYT/Au complex compared to clean Au nanosurface was 9 nm and the presence of Ag as a sublayer in the CYT/Au/Ag complex increased the magnitude of this shift to 34 nm compared to clean Au/Ag nanosurface. It was seen that the Ag sublayer increased this shift in the CYT/Au/Ag complex compared to that in the CYT/Au complex while when Au was used as the sublayer in the CYT/Ag/Au complex, this shift was less in magnitude in comparison with the CYT/Ag complex. The other important point is that the presence of the CYT in the CYT/Ag/Au complex increased the intensity of absorption spectrum compared to clean Ag/Au nanosurface while the opposite trend was seen in the CYT/Au/Ag compared to Au/Ag nanosurface. Figure 5a compares the TDOS of CYT/Ag/Au complex and the PDOS of Ag and Au in this structure with those of the clean Ag/Au to see the effect of the CYT on the contribution of Au and Ag fragments in the TDOS of the CYT/Ag/Au. As seen, the adsorption of CYT on Ag/Au nanosurface caused the increase of PDOS of Au in the range of 0 to 10 eV while the PDOS of Ag decreased in this range compared to those in the Ag/Au nanosurface. This meant that the presence of CYT in CYT/Ag/Au increased the contribution of Au fragments in the unoccupied states in the


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range of 0 to 10 eV. Also, it was seen that there is no change in the PDOS of Ag and Au in the energy range related to the occupied states (below -5 eV) due to the presence of CYT. The adsorption of the CYT on the Ag/Au nanosurface caused the increase of the TDOS of the CYT/Ag/Au complex compared to that of clean Ag/Au nanosurface in the energy range higher than 0 eV related to the unoccupied states which meant that the number of unoccupied states of CYT/Ag/Au complex is more than that of Ag/Au nanosurface in this energy region. The reason for this increase was due to the mixing of the unoccupied states of Ag/Au nanosurface with the unoccupied states of CYT which was accompanied with the increase in the number of states of CYT/Ag/Au complex compared to that of Ag/Au nanosurface in this energy region. The increase of the number of unoccupied states of CYT/Ag/Au complex caused the decrease of the energy gap between its unoccupied states compared to Ag/Au nanosurface. In this case, it was expected that the number of electronic transitions from the occupied states to unoccupied states increased in the CYT/Ag/Au complex compared to clean Ag/Au nanosurface. This increase has also been shown in the inset of Figure 2 so that the number of allowed electronic transitions of the CYT/Ag/Au complex were considerably greater than those of the Ag/Au nanosurface. In fact, the presence of CYT in the CYT/Ag/Au complex increased the number of allowed electronic transitions, especially in higher wavelengths compared to Ag/Au nanosurface and led to the increase of the intensity of the absorption spectrum of the CYT/Ag/Au complex compared to the spectrum of Ag/Au nanosurface, as shown in Figure 2. The presence of the CYT in the CYT/Au/Ag complex did not induce significant changes in the PDOS of Ag and Au compared to those of clean Au/Ag nanosurface (see Figure 5b). This meant that the contribution of Au and Ag fragments in the states of the CYT/Au/Ag complex was not as affected by the interaction of CYT with the Au/Ag nanosurface unlike to what was observed



for the CYT/Ag/Au complex compared to Ag/Au nanosurface in Figure 5a. Figure 5b also shows that the presence of the CYT in the CYT/Au/Ag complex increased the TDOS of the complex in the energy region of 0 to 40 eV compared to clean Au/Ag nanosurface. This meant that the number of unoccupied states of the CYT/Au/Ag complex was more than the number of unoccupied states of Au/Ag nanosurface in this energy region due to the mixing of the states of CYT with the states of nanosurface. The increase of the unoccupied states in the CYT/Au/Ag complex was accompanied with the increase of allowed electronic transitions compared to clean Au/Ag surface. The inset of Figure 3 shows the increase of allowed transitions of the CYT/Au/Ag complex compared to Au/Ag nanosurface for the wavelengths higher than 550 nm which led to the shift of the absorption spectrum of the CYT/Au/Ag complex to the higher wavelength. It is important to note that although the presence of CYT in the CYT/Au/Ag complex increased the number of allowed transitions, it decreased the oscillator strength of some transitions which in turn led to the decrease of the intensity of its absorption spectrum compared to the spectrum of Ag nanosurface. Figure 2 also compares the absorption spectrum of Ag nanosurface with that of CYT/Ag complex. It is seen that the intensity of absorption spectrum of CYT/Ag complex increased and the maximum of absorption spectrum shifted to the higher wavelength compared to clean Ag nanosurface. The inset of this figure showed that the presence of CYT increased the number of allowed transitions of the CYT/Ag complex. Figure 6a compared the DOS of Ag nanosurface with the TDOS of CYT/Ag complex. It was seen that the presence of CYT increased the TDOS of CYT/Ag complex in the energy region of unoccupied states which was in agreement with the increase of the intensity of absorption spectrum of the CYT/Ag complex compared to Ag nanosurface. Also, it was seen that the PDOS of Ag in the CYT/Ag complex was nearly matched to the DOS of clean Ag nanosurface. In the case of Au nanosurface and CYT/Au complex, the


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increase of the intensity of the absorption spectrum of CYT/Au complex and its shift to the higher wavelength compared to the spectrum of Au nanosurface were small (see Figure 3).Similar to CYT/Ag, the adsorption of CYT on the Au nanosurface increased the DOS of the unoccupied states compared to Au nanosurface (see Figure 6b).



8


(a) TDOS of CYT/Ag/Au

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PDOS of Au fragment PDOS of Ag fragment


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Energy (eV) Figure 5. (a) The calculated total density of states (TDOS) and partial DOS (PDOS) of the CYT/Ag/Au complex (dashed line curves) and Ag/Au nanosurface (solid line curves). (b) The calculated TDOS and PDOS of the CYT/Au/Ag complex (dashed line curves) and clean Au/Ag nanosurface (solid line curves).


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10

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40

Energy (eV)


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


8

(b)

TDOS of CYT/Au PDOS of Au PDOS of CYT DOS of Au

6

4

2

0 -10

0

10

20

30

40

Energy (eV) Figure 6. (a) The calculated total density of states (TDOS) and partial DOS (PDOS) of CYT/Ag and clean Ag nanosurface. (b) The calculated TDOS and PDOS of CYT/Au and clean Au nanosurface.



(c) The effect of sublayer on the charge transfer electronic transitions In this part, the effect of sublayer on the charge transfer electronic transitions in the calculated absorption spectra is discussed. It is important to note that the charge transfer from the adsorbate to substrate increases the electric field near the metal surface for both incoming and scattered radiation which causes the SERS. Therefore, knowing the position of the charge transfer electronic transitions and their variation with sublayer is very important for generating the SERS spectra in these kind of nanostructures. A brief investigation on the main electronic configuration of the calculated electronic transitions of CYT/Au and CYT/Au/Ag complexes showed that the HOMO and HOMO-1 of the CYT contributed to the charge transfer from the CYT to nanosurface upon electron excitation. The HOMO-9 and HOMO-24 of the CYT/Au complex are corresponding to the HOMO and HOMO-1 of the CYT, respectively (see Figure 7). The shape of the electron density localized on the CYT in the HOMO-9 and HOMO-24 of the CYT/Au complex is the same as the electron density of HOMO and HOMO-1 of isolated CYT. Similarly, the HOMO-10 and HOMO-18 of the CYT/Au/Ag are corresponding to the HOMO and HOMO-1 of isolated CYT, respectively. Figure 7 shows the molecular orbitals of the CYT/Au contributing to the charge transfer electronic transitions. As can be seen, there are four electronic transitions located at 658.95 (HOMO-9  LUMO+3), 728.07 (HOMO-9  LUMO+2), 793.32 (HOMO-9 LUMO+1) and 865.92 nm (HOMO-9 LUMO) in the calculated absorption spectrum of CYT/Au containing the charge transfer from the HOMO of CYT to Au nanosurface. The electronic transitions containing the charge transfer from the HOMO-1 of the CYT to surface are located at 596.52 (HOMO-24 LUMO+1), 596.26 (HOMO-24 LUMO+1), 594.69 (HOMO-24 LUMO+1), 636.90 (HOMO-24 LUMO) and 636.14 nm (HOMO-24 LUMO). The percentage of the charge transfer in each electronic transitions has also been identified in Figure 7. It is seen that the


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electronic transitions located at 728.07 and 865.92 nm are mainly related to the charge transfer from the CYT to Au nanosurface with the percentage of 92 and 89%, respectively. The presence of Ag sublayer causes that the electronic transitions containing the charge transfers to move to the shorter wavelength. In addition, the number of electronic transitions, containing the charge transfer from the HOMO-1 of CYT to the LUMO and LUMO+1 of the nanosurface decreases in the CYT/Au/Ag compared to CYT/Ag complex. A brief investigation on the main electronic configuration of the calculated electronic transitions of the CYT/Ag and CYT/Ag/Au complexes showed that only the HOMO of the CYT contributed to the charge transfer from the CYT to nanosurface upon electron excitation. In the CYT/Ag complex, the HOMO-13 of the complex has contribution from the HOMO of CYT. Two molecular orbitals of CYT/Ag/Au complex including HOMO-20 and HOMO-21 have contribution from the HOMO of CYT. Figure 8 shows that there are four transitions with the main electronic configurations containing the charge transfer from the HOMO of CYT (HOMO-13 of CYT/Ag) to the Ag nanosurface. The wavelength of each transition and its charge transfer percentage have also been reported in Figure 8. The presence of Au sublayer caused the number of charge transfer electronic transitions to decrease in the CYT/Ag/Au complex compared to CYT/Ag complex but the percentage of charge transfer of each transition to increase. Comparison of Figure 8 with 7 shows that the charge transfer from the CYT to nanosurface take places from the HOMO and HOMO-1 of CYT in the CYT/Au and CYT/Au/Ag complexes while in the CYT/Ag and CYT/Ag/Au the charge transfer is only from the HOMO of CYT to nanosurface.



Page 78 of 106

LUMO+3 LUMO+3

LUMO+2

LUMO+2 HOMO-9 HOMO-10

LUMO+1

LUMO+1

LUMO LUMO

LUMO+1

HOMO-24

LUMO+1

HOMO-18

LUMO

CYT/Au

LUMO

CYT/Au/Ag

Figure 7. The molecular orbitals of the CYT/Au and CYT/Au/Ag complexes contributing in the charge transfer from the CYT to nanosurface during electron excitation. The wavelength and percentage of charge transfer for each electronic transitions have been identified. The HOMO-9 and HOMO-24 of the CYT/Au complex are corresponding to the HOMO and HOMO-1 of the isolated CYT. Similarly, the HOMO-10 and HOMO-18 of the CYT/Au/Ag complex are corresponding to HOMO and HOMO-1 of isolated CYT.


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LUMO+1

HOMO-20

HOMO-13

LUMO

LUMO

CYT/Ag

HOMO-21

CYT/Ag/Au

Figure 8. The molecular orbitals of the CYT/Ag and CYT/Ag/Au complexes contributing in the charge transfer from the CYT to nanosurface during electron excitation. The wavelength and percentage of charge transfer for each electronic transitions have been identified. The HOMO-13 of the CYT/Au complex is corresponding to the HOMO of the isolated CYT. Two molecular orbitals of the CYT/Au/Ag complex including HOMO-20 and HOMO-21 have contribution from the HOMO of isolated CYT. (d) Comparison of IR spectra Most of the vibrational spectroscopic studies related to the adsorption of DNA bases on metal nanostructures are often related to the SERS and not IR spectroscopy. Ataka and Osawa have studied the adsorption of CYT on a gold electrode at different potentials and recorded the IR spectrum of CYT at different electrode potentials to obtain information about the adsorption geometry of the CYT on the electrode surface.60 Figure 9a compares the calculated IR spectrum of CYT in the CYT/Au complex with that in the CYT/Au/Ag complex to see the effect of Ag sublayer on the IR spectrum of CYT. The presence of Ag as a sublayer in the CYT/Au/Ag complex causes considerable changes in the IR spectrum of CYT compared to that in the CYT/Au complex in the range of 500 to 1000 cm-1. The peak of highest intensity in the IR spectrum of CYT/Au



complex is peak No.1 located at 513.224 cm-1 related to the wagging of one of the H atoms of NH2 group (see Figure 10a). In the IR spectrum of CYT/Au/Ag complex, this peak shifts to the lower wavenumber (476.759 cm-1) and the wagging of two H atoms of NH2 group takes place in the vibrational mode of this peak. The other important change in the IR spectrum of CYT due to Ag sublayer is the increase of the energy gap between peaks No. 2 and 3 in the IR spectrum of CYT/Au/Ag complex compared to the CYT/Au complex. The peaks No. 2 and 3 in the IR spectrum of CYT/Au complex are mainly related to the wagging of one of the H atoms of NH 2 group, wagging of the N-H and C-H of CYT ring. The presence of Ag sublayer causes the wagging of the second H atom of NH2 group of CYT to become active in the CYT/Au/Ag complex. It can be concluded that the Ag sublayer activates the wagging of both H atoms of the NH 2 group of the CYT related to peaks No. 1, 2 and 3. The other important change in the IR spectrum of CYT due to the Ag sublayer is seen in the range of 3000 to 4000 cm-1. The Ag sublayer shifts the vibrational peak, related to the N-H stretching of the NH group of CYT ring in the plane of the molecule, to the higher wavenumber. Figure 9b compares the IR spectrum of CYT in the CYT/Ag complex with that in the CYT/Ag/Au complex. The peak No.1 (437.051 cm-1) in the IR spectrum of CYT/Ag complex is mainly related to the wagging of one of the H atoms of the NH2 group from the plane of the molecule (see Figure 10b). The presence of Au sublayer shifts this peak to a higher wavenumber (467.349 cm-1) in the spectrum of the CYT/Au/Ag complex. Two vibrational bands with relatively similar intensities are seen in the IR spectrum of the CYT/Ag/Au system in the range of 500 to 600 cm-1 (peaks No. 2 and 3 in Figure 9b). The peak No.2 is related to the wagging of H atoms of the NH2 group from the plane of the molecule so that the displacement of one of the H atoms is greater than the other. Peak No.3 is related to the wagging of one of the H atoms of the NH2 group


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and N-H group of the ring, simultaneously. The important difference between the IR spectrum of CYT/Ag and CYT/Ag/Au is related to the region of 500 and 600 cm -1. The Au sublayer causes the intensity of peak No.2 in the spectrum of the CYT/Ag complex to increase considerably in the spectrum of CYT/Ag/Au without any energy shift. Also, Peak No.3 in the spectrum of CYT/Ag shifts to the lower wavelength and its intensity decreases in the spectrum of CYT/Ag/Au complex. Peak No.4 in the IR spectrum of CYT/Ag/Au complex is only related to the wagging of N-H of the ring. The Au sublayer shifts this peak to the lower wavelength in the spectrum of the CYT/Ag/Au complex. Peak No. 5 in the spectrum of CYT/Ag and CYT/Ag/Au complexes is mainly related to the N-H stretching of NH2 group of CYT and Au sublayer shifts this peak to higher wavelength and decreases its intensity.



Intensity (arb.uni)

1400

(a)

40

1

CYT/AuAu CYT/Au/Ag Ag-Au

1200 1000

30

800 20

1

600

4

3 2

4

400

10

200

2

3

0

0 4000 3800 3600 3400 3200 3000

2000

1500

1000

500

0

Wavenumber (cm-1) 50

1

5

(b) Intensity (arb.uni)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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CYT/Ag Ag CYT/Ag/Au Au-Ag

500

40

3 4

1

4

30

5

400 300

20

2 3

200

10

100

0

0

2

4000 3800 3600 3400 3200 3000

2000

1500

1000

500

Wavenumber (cm-1)

Figure 9. (a) The calculated IR spectrum of CYT on the Au (blue spectrum) and Au/Ag nanosurfaces (red spectrum). (b) The calculated IR spectrum of CYT on Ag (blue spectrum) and Ag/Au nanosurfaces (red spectrum). Comparison of intensity and position of the vibrational bands with the same numbering shows the difference between the IR spectra due to the sublayer.


0

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CYT/Au/Ag (3)

(4)

(1)

(2)

CYT/Au (3)

(4)

(1)

(2)

(a) CYT/Ag/Au (5)

(4)

(3)

(5)

(4)

(3)

(2)

(1)

CYT/Ag (2)

(1)

(b)

Figure 10. (a) The vibrational modes of the peak numbered in the IR spectrum of CYT/Au and CYT/Au/Ag in Figure 9a. (b) The vibrational modes of the peak numbered in the IR spectrum of CYT/Ag and CYT/Ag/Au in Figure 9b. The white, gray, blue and red balls show the H, C, N and O atoms, respectively.



(e) Comparison of Raman spectra In this part, the normal Raman and the SERS spectra of CYT adsorbed on the selected nanosurfaces are calculated and analyzed. The SERS spectra were calculated using the TD-DFT method in the infinite lifetime approximation at the wavelengths near the absorption lines corresponding to the charge transfer from the CYT to nanosurfaces. Although, within the infinite lifetime approximation, the actual changes in the intensity of each vibrational band cannot be estimated, the relative intensities of vibrational bands are accurate and comparable with the relative intensities of vibrational bands in the SERS spectra79 calculated using the finite lifetime damping. It is important to note that three effects including (a) the surface plasmon resonance (SPR), (b) photo-induced charge transfer (CT), and (c) molecular resonance (MR) are responsible for the intensity enhancement of vibrational bands in the SERS spectrum. It is very difficult to separate the contribution of each mechanism by purely experimental means and consequently, the quantum chemical calculations are necessary. Although, there are several papers in the literature 51-76 on the SERS of DNA bases adsorbed on different metal nanostructures, especially, Ag, Au, and their bimetallic nanostructures, the charge transfer enhancement contribution in the SERS has not been studied for the DNA bases on metal surfaces. It is important to note that the absorption lines that are appropriate for our calculations are those with no other absorption lines near them. It is possible to easily pick a wavelength higher or lower than the target wavelength. In this case, the pure effect of charge transfer on the Raman spectra of CYT on the selected nanosurfaces and the vibrational modes showing intensity enhancement due to the charge transfer can be determined. To the authors, knowledge, there is no experimental and theoretical study on the SERS spectra of CYT on these surfaces due only to the charge transfer from the CYT to nanosurface.


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The vibrational modes of CYT showing intensity enhancement in the SERS spectra are determined for each nanosurface. As mentioned, there were some absorption lines in the UV spectra of CYT/Ag, CYT/Ag/Au, CYT/Au and CYT/Au/Ag complexes related to the charge transfer from the CYT to nanosurface (see Figures 7 and 8). The absorption lines located at 865.92 and 728.07 nm are appropriate for calculating the SERS spectra of CYT/Au structure because there is no other absorption line near them and the intensity enhancement is mainly due to the charge transfer from the CYT to nanosurface. Therefore, the SERS spectra of the CYT/Au structure were calculated at two wavelengths including 873.92 and 725.925 nm, separately. The selected wavelength for the CYT/Au/Ag structure was 713.51 nm. The SERS spectra of the CYT/Ag were calculated at two different wavelengths including 496.50 and 494.585 nm. Only one SERS was calculated for CYT/Ag/Au system at a wavelength of 502.77 nm. To obtain the intensity of each vibrational band in the SERS spectrum, the calculation of the Raman activity (Sj) of the related vibrational mode is necessary. For this purpose, the TD-DFT method was used for the calculation of the Sj of each vibrational mode at each selected wavelength. The calculated value of Sj for each vibrational mode was used in the following relationship to calculate the Raman intensity. 51  

=

𝑆 = 45





 

+7





(1)

𝑆



(2)

where σ is the Raman cross-section, Ω is the depolarization ratio, o is the frequency of the incident light which is corresponding to the wavelength selected from the absorption spectrum, ν j is the frequency of the vibrational mode, c is the velocity of light, α is the polarizability, γ is the anisotropic polarizability, and Qj is the normal coordinate. The normal Raman spectra were



calculated using the normal Frequency calculations in G09 package considering static electric dipole approximation. Figures 11a and 11b demonstrate the SERS of CYT/Au complex, calculated at 725.925 and 873.92 nm, respectively (black spectra) and compare them with the calculated normal Raman spectrum of CYT/Au complex (blue spectra). As seen in Figure 11b, the intensity enhancement is seen for four vibrational bands located in the range of 1300 to 1800 cm -1 (1356.17, 1489.17, 1638.95 and 1686.88 cm-1) at 873.92 nm. These vibrational bands have been numbered in Figure 11a (peaks No.1 to 4). When the wavelength shift to 725.925 nm, the enhancement of intensity is seen only for two vibrational bands located at 1356.17 and 1489.17 cm -1 (peak No.1 and 2). It is important to note that the wavelength of 873.92 nm is near the 865.92 nm which corresponds to electron excitation from HOMO-9 to LUMO while the wavelength of 725.925 nm is near the 728.07 nm which is corresponding to the electron excitation from HOMO-9 to LUMO+2. The vibrational modes related to the vibrational bands numbered in Figure 11b for CYT/Au have been shown in Figure 12. Figure 11c compares the SERS spectrum of CYT/Au/Ag system calculated at 713.51 nm with its normal Raman spectrum. As seen, the enhancement of intensity is seen for three vibrational bands which have been numbered in the spectrum. Peak No. 1, 2 and 3 have been located at 1354.26, 1489.25 and 1635.33 cm-1, respectively, and their vibrational modes have been shown in Figure 12. Comparison of Figure 11c with 11a and 11b shows that the presence of Ag sublayer caused the Raman shift of peaks No.1, 2 and 3 to move slightly to the lower wavenumber. Figure 11 shows that peak No.1 and 2 in the Raman spectra of the CYT/Au and CYT/Au/Ag complexes show more sensitivity for intensity enhancement due to the charge transfer from the CYT to the nanosurfaces compared to the other vibrational bands. Therefore, peak No.1 and 2 could be selected as reference vibrational bands for the charge transfer effect. The other important


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point is that the displacement of the atoms in the vibrational mode related to peak No.2 changes in the CYT/Au/Ag complex compared to the CYT/Au complex so that the stretching of the C-N bond of the ring of CYT is added to the vibrational mode of this peak in the CYT/Au/Ag complex.



Page 88 of 106

2 CYT/Au/Ag

=713.51 nm

1 3

(c)

2000

1800

1600

1400 2

CYT/Au

4

1200

1000

800

600

=873.92 nm

1

3

(b)

2000

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1600

1400

1200

1000

800

600

2

CYT/Au

=725.92 nm 1

(a)

2000

1800

1600

1400

1200

1000

800

600

Raman Shift (cm-1)

Figure 11. Comparison of the calculated SERS spectra of CYT (black spectrum) (a) at 725.92 nm for CYT/Au (b) at 873.92 nm for CYT/Au and (c) at 713.51 nm for CYT/Au/Ag. The blue spectrum in (a) and (b) are the same and it is the normal Raman spectrum of CYT in CYT/Au. The blue spectrum in (c) is the normal Raman spectrum of CYT in CYT/Au/Ag.


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CYT/Au 873.92 nm

(1)

(2)

(3)

(2)

(3)

(4)

CYT/Au/Ag

(1)

Figure 12. The vibrational modes related to the vibrational bands showing intensity enhancement numbered in Figure 11b and 11c for CYT/Au and CYT/Au/Ag, respectively. Figures 13a and 13b compare the calculated SERS spectrum of CYT/Ag calculated at the wavelengths of 494.59 and 496.50 nm, respectively. It is seen that the change of wavelength from 494.59 to 496.50 nm creates considerable changes in the intensity enhancement of vibrational bands. When the selected wavelength is 494.59 nm, the enhancement of the vibrational bands takes place in the range of 600 to 800 cm-1 and 1400 to 1800 cm-1. The enhancement of the vibrational bands occurs in the range of 1400 to 1800 cm-1 at 496.50 nm. The vibrational bands in the Raman spectrum of CYT/Ag system showing considerable intensity enhancement have been numbered in Figure 13a and 13b. These vibrational bands in Figure 13a have been located at 625.14, 778.887, 1633.47 and 1675.38 cm-1 and their related vibrational modes have been shown in Figure 14. The vibrational bands numbered in the Raman spectrum of CYT/Ag calculated at 496.50 nm are at 1558.06 and 1680.39 cm-1. Based on Figures 13a and 13b, the vibrational bands located in the range of 1550 to 1700 cm-1 are good candidates for the SERS effect due to the charge transfer from



the CYT to Ag nanosurface. In the presence of Au sublayer, there are two absorption lines mainly related to the charge transfer from the CYT to surface located at 503.35 and 509.76 nm. The absorption line located at 503.35 nm is appropriate for calculating the SERS spectrum because of the absence of absorption lines related to the excitation of the surface near it. Figure 13c compares the SERS spectrum of CYT/Ag/Au calculated at 502.77 nm. It is seen that the enhancement of intensity takes place mainly for two vibrational bands located at 617.244 (peak No.1) and 944.339 (peak No.2) cm-1. The vibrational mode of peak No.1 is related to the out of plane bending of NH of the ring and the vibrational mode of the second peak is related to the out of plane bending of C-H bonds of the ring.


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=502.77 nm

CYT/Ag/Au 2

1

(c)

2000

1800

1600

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1

CYT/Ag

800

600

=496.50 nm

2 (b)

2000

1800

CYT/Ag

1600

4

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1000

3

800

2

600

=494.59 nm 1

(a)

2000

1800

1600

1400

1200

1000

800

600

Raman Shift (cm-1)

Figure 13. Comparison of the calculated SERS spectra of CYT (black spectrum) (a) at 494.59 nm for CYT/Ag (b) at 496.50 nm for CYT/Ag and (c) at 502.77 nm for CYT/Ag/Au. The blue spectrum in (a) and (b) are the same and it is the normal Raman spectrum of CYT in CYT/Ag. The blue spectrum in (c) is the normal Raman spectrum of CYT in CYT/Ag/Au.



Page 92 of 106



CYT/Ag 494.59 nm

(1)

(2)

(3)

(4)

CYT/Ag 496.50 nm

(2)

(1) CYT/Ag/Au (1)

(2)

Figure 14. The vibrational modes related to the vibrational bands showing intensity enhancement numbered in Figure 13 for CYT/Ag and CYT/Ag/Au.

Conclusion The experimental UV absorption spectra of different nanostructures composed of Au and Ag metals, especially in the form of pure and bimetallic core-shell nanoparticles, have been reported in literature and the change in the maximum position and intensity of their absorption spectra with the percentage of Ag and Au in the core-shell nanoparticles have been demonstrated, without any theoretical reasons for the changes. Therefore, in the first part of this work, the pure and bimetallic nanosurfaces of Ag and Au metals were used as a model to interpret the experimental results. The theoretical results showed that the presence of Au sublayers in the


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Ag/Au nanosurface increases the intensity of absorption spectrum considerably and shifts the maximum of absorption spectrum to higher wavelength compared to Ag nanosurface. In the case of Au/Ag nanosurface, the Ag sublayer increases the intensity of absorption spectrum and shifts it to the lower wavelength compared to Au nanosurface. The calculations showed that the presence of sublayer in nanosurface increases the number of allowed electronic transitions compared to pure nanosurface which is accompanied with the increase in the intensity of absorption spectrum. To interpret the variations observed in the absorption spectra due to the sublayer, the TDOS of the bimetallic nanosurfaces were calculated and compared with the DOS of pure nanosurfaces. Comparing of the TDOS of Ag/Au nanosurface with that of pure Ag nanosurface showed a decrease in the intensity of the TDOS of Ag/Au nanosurface in the energy region related to the occupied states along with a small shift to more negative energy. Also, it was observed that the Au sublayer did not nearly have effect on the TDOS of unoccupied states in the region of -2.5 to 7.5 eV which meant that the number of unoccupied states in this energy region were nearly constant. Based on these comparisons, it was concluded that the main reason for the increase of intensity and shift of the maximum of absorption spectrum of Ag/Au nanosurface to higher wavelength is the allowance of many electronic transitions which were forbidden in the Ag nanosurface. Comparison of the TDOS of Au/Ag nanosurface with that of Au nanosurface showed that the intensity of peak of TDOS related to the occupied states of Au/Ag increased compared to pure Au surface and shifts to more negative energy which this energy shift was considerably more than that observed for the Ag/Au nanosurface compared to Ag nanosurface. This increase showed that the occupied states of the Au/Ag nanosurface became closer to each other compared to Au nanosurface due to the Ag sublayer. Similar to the Ag/Au nanosurface, the presence of Ag sublayer in the Au/Ag nanosurface did not change the number of unoccupied states of nanosurface in the



energy range of -2.5 to 7.5 eV because of the small changes in the TDOS of the nanosurface compared to pure Au nanosurface. The shift of the absorption spectrum of the Au/Ag nanosurface compared to Ag nanosurface was attributed to the increase of the energy separation between the occupied and unoccupied states. The interaction of the CYT with the nanosurfaces shifted their absorption spectra to the higher wavelength compared to clean nanosurfaces. The presence of the CYT in the CYT/Ag/Au complex increased the intensity of its absorption spectrum compared to clean Ag/Au nanosurface while the opposite trend was seen for the CYT/Au/Ag complex compared to Au/Ag nanosurface. It was found that the adsorption of CYT on the Ag/Au nanosurface increased and decreased the contribution of Au and Ag in the unoccupied states compared to clean Ag/Au nanosurface, respectively. In the CYT/Au/Ag, the presence of the CYT does not provide significant changes in the PDOS of Ag and Au compared to those of clean Au/Ag nanosurface. It was seen that the interaction of the CYT with nanosurfaces in the CYT/Au/Ag and CYT/Ag/Au complexes increased their TDOS in the energy region related to the unoccupied states. The decrease of the intensity of the maximum of absorption spectrum of the CYT/Au/Ag complex compared to Au/Ag nanosurface, in spite of the increase of the number of its allowed transitions, was attributed to the decrease of the oscillator strength of its electronic transitions. In the second part of this work, the effect of sublayer on the IR and Raman spectra of CYT was studied and the vibrational modes discriminating this effect were determined. Comparison of the IR spectra of CYT in the CYT/Au and CYT/Ag complexes with those in the CYT/Au/Ag and CYT/Ag/Au complexes, respectively, showed that the vibrational peaks sensitive to the sublayer have been located in the range of 400 to 1000 cm-1 and mainly related to the wagging of the hydrogen atoms of NH2 group, C-H and N-H of the ring. The other region in the IR spectrum


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which reflects the effect of sublayer is the region of 3400 to 3800 cm -1. The Ag sublayer in the CYT/Au/Ag complex causes the peak related to the stretching of N-H to moves to a higher wavenumber. In the presence of Au sublayer in the CYT/Au/Ag complex, the vibrational mode related to the symmetry stretching of the NH2 group moved to a lower wavenumber. The charge transfer SERS spectra of the CYT when adsorbed on the selected nanosurfaces were also calculated. The selected excitation wavelengths for calculating the SERS spectra were close to the wavelength related to the charge transfer from the CYT to nanosurface. The vibrational modes of the CYT represented by Raman peaks allowed the intensity enhancement due to the charge transfer to be determined for each nanosurface. It was observed that for the CYT/Au and CYT/Au/Ag complex, the peaks showing enhancement intensity have been located in the range of 1300 to 1800 cm-1 and the Ag sublayer increased the enhancement intensity of some vibrational bands compared to what was observed for the CYT/Au complex in this region of wavenumber. The presence of Au sublayer in the CYT/Ag/Au complex changes the patterns the SERS spectrum of the CYT considerably compared to what was observed for CYT/Ag (enhancement occurring in the 600 to 1000 cm-1 region).



Acknowledgement The authors thank to Isfahan university of technology (IUT) for its financial support. Also, the authors gratefully acknowledge the Sheikh Bahaei National High Performance Computing Center (SBNHPCC) for providing computing facilities and time.


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Associated Contents Supporting Information Explanations about the preparation and optimization of the Au, Ag, Ag/Au and Au/Ag nanosurface and their complexes with CYT performed in our previous work (reference 40) Author information Corresponding Author *Tel: +98 31 33913243. Fax: +98 31 33912350. E-mail: [email protected] ; [email protected]

Notes The authors declare no competing financial interest.



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TOC Graphic

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UV, IR, and Charge Transfer SERS Spectra - ACS Publications

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