DFT and SERS Study of L-Cysteine Adsorption on the Surface of Gold

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C: Surfaces, Interfaces, Porous Materials, and Catalysis

DFT and SERS Study of L-Cysteine Adsorption on the Surface of Gold Nanoparticles Guohua Yao, and Qing Huang J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b00949 • Publication Date (Web): 24 May 2018 Downloaded from http://pubs.acs.org on May 24, 2018

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The Journal of Physical Chemistry

DFT and SERS Study of L-cysteine Adsorption on the Surface of Gold Nanoparticles Guohua Yao1 and Qing Huang1,2* 1

Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China 2 University of Science & Technology of China, Hefei 230026, China *Corresponding author: [email protected]

Abstract Both surface enhanced Raman spectroscopy (SERS) experiments and density functional theory (DFT) calculations have been carried out to investigate adsorption of cysteine on gold nanoparticle surface. Cysteine is one of the amino acids which have a rotating dihedral angle and several possible adsorption sites, so there could be many possible adsorption conformations. At present, the adsorption conformation of cysteine on the gold surface has not been solved, although previous work had explored the conformations based on DFT method, but no explicit experimental evidence was provided. Nevertheless, the previous work had indicated that the adsorption conformations of some simple rigid molecules on the surface of metal nanoparticles could be identified through SERS experimental data. Therefore, in this work, we attempted to figure out the conformation and adsorption sites of the flexible typical amino acid cysteine on gold nanoparticle surface by combining both DFT and SERS methods. We found that the adsorption of cysteine on the surface gold nanoparticle adopted the most predominant configuration in which cysteine chemically interacted with Au cluster through both S and O sites with cysteine taking the configuration of a gauche position for the protonated amino group and an anti-position for the carboxylate group in the molecule.

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Introduction The strong adsorption of cysteine on gold surface has been widely used in many fields. Proteins or DNA strands can be attached to gold nanostructures through cysteine-gold interactions.1 These modified metallic surfaces may find significant technological applications in chemical-specific detection, sensing and catalysis.2 For example, Gold nanostars coated with cysteine were synthesized and applied in SERS-based copper ions (Cu2+) detection in aqueous media.3 Gold nanoparticle-based colorimetric competition assay was applied in the detection of cysteine based on the interaction between cysteine and gold nanoparticles.4 So, it is necessary to have a better understanding of the molecular properties of the adsorption of cysteine and other amino acids on metal surfaces, and in fact, many theoretical or experimental works have been reported.1-2 Canepa et al. have studied the vapor-phase deposition of L-cysteine (L-cys) on the Au (110) surface by means of synchrotron-based techniques, X-ray photo-emission and CK-shell X-ray absorption spectra, and the molecules were found to lay flat on the surface with both the Cβ-S bond and the carboxylic group almost parallel to the surface.5 Marek Graff et al. reported the adsorption of enantiomeric and racemic cysteine on a silver electrode–SERS sensitive to chirality of the adsorbed molecules.6 In addition, electrochemistry of L-cys on several types of electrode materials has been extensively investigated.2, 7 And the characterization of L-cys adlayers on Au (111) has also been provided using in situ (in an electrochemical environment) scanning tunneling microscopy (STM).8

Figure 1 The Newman projections (left) and the labeling of atoms for the structures of cysteine-gold cluster model (right). Until now, however, the microstructures of the interactions between the amino acids (include cysteine) and the metal nanoparticles are basically still elusive. Since cysteine has a rotable χ1(S-Cβ-Cα-Cγ) torsional angle (Figure 1), three conformers (PH, PC, PN) of cysteine may exist. Considering that the sulfur atom is attached to the surface, we consider that three conformations are possible for the relative orientations of the amino and the carboxylate groups. The Newman projections of these rotamers are presented in Figure 1. But it is not clear which conformation is present when cysteine is adsorbed onto the gold surface. It is known that there is strong chemisorption between cysteine and metal surface through thiol group. Stewart and Fredericks concluded that the ionized carboxylate group and the protonated amino group were also in close contact with the surface.9 But it has not been determined whether the amino group or carboxyl group is chemically adsorbed on the substrate. When cysteine is adsorbed on the gold nanoparticles, SERS signals can be detected, and the SERS


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spectra can provide a lot of structural information. The influence on the SERS spectral pattern from the chemical effect can be crucial for identifying the molecular sites involved in the chemical interaction with the substrate. In the past, the adsorption behavior of cysteine in gold colloidal solution was studied according to the ‘‘surface selection rules’’ for analyzing of the SERS spectra.10-11 The SERS signals of cysteine including some SERS bands from sulfur, NH3+ and COOgroups are enhanced; reaching the conclusion that cysteine molecule interacts with the metal surface simultaneously through sulfur, NH3+ and COO- groups.10 Compared with the normal Raman spectra, the wavenumbers of SERS bands are normally shifted when the molecule is adsorbed to the metal surface. So it is still a challenge to assign the SERS bands for determining the involved conformations. With the help of the DFT calculation of the molecule-metal cluster, the chemical interaction between the molecule and substrate can be properly described. The structure of molecule-metal cluster system and the assignment the vibrational modes can be more accurately determined if one can figure out the molecular conformation and the interaction between the molecule and the adsorbing metal. DFT calculations of molecule-cluster models have been effectively used for the simulation of SERS spectra of small molecules adsorbed on the silver and gold surfaces, such as adenine, p-aminothiophenol, benzyl Chloride and methimazole.12-16 In principle, through comparison between the theoretical computation and the experimental SERS spectra, the adsorption of molecule on the surface of the metal can be analyzed and the adsorption conformation can be determined. Actually, there have been some former DFT studies on cysteine adsorbed on metal surfaces,17-18 though with the energy analysis mainly used for estimation of the adsorbing structure. Cordeiro et al. employed the DFT method to study of the adsorption of D‑(L-) cysteine on flat and chiral stepped gold surfaces (Au (321) R, S and Au (111)).17 They concluded that the adsorption occurred with the cysteine bound to the surface through only one contact point (by its sulfur atom). However, there was no comparison between theory and experiment, so it was still difficult to decide the corresponding conformation.17 In this work, density functional theory (DFT) with the M06-2X functional was used for the optimization of the ground state geometries and simulation of the vibrational spectrum of this amino acid. The SERS spectrum with a large silver cluster as a model metallic surface was simulated previously.19 The 18-atom neutral silver cluster was constructed as a closed-shell singlet based on the experimental bulk geometry data with 12 atoms on the surface plane and 6 atoms on a parallel lower layer, representing the Ag [110] surface. But Z-matrix of the parallel was constrained, so it could not reasonably simulate the chemisorption between cysteine and metal. To the best of our knowledge, this is the first research using this molecule-metal cluster model to simulate amino acids (include cysteine) and gold substrate, in which we also compared the DFT calculation with the experimental SERS spectra in order to determine and understand the involved chemical interactions. The focus of the present work was therefore to obtain information on the adsorption behavior of the L-cysteine molecules on gold nanoparticles, and to achieve the vibrational characterization of the adsorbed molecule as well.



Experimental Section Materials L-cysteine (noted as “cysteine” or “cys” in this work), gold acid chloride trihydrate (HAuCl4·3H2O), sodium citrate, sodium borohydride (NaBH4) were purchased from Sigma-Aldrich. High purity water was used in this work. All the chemicals were used without further purification. Fabrication of gold nanoparticles The aqueous solutions of gold colloids were prepared by two typical methods. (a) In the first method, the gold colloids were prepared by the method described by Creighton et al.20 The aqueous solution of gold colloids were prepared by reduction of 20 mL of 2x10-3 M HAuCl4·3H2O with ice-cold 60 mL of 2.0x 10-3 M NaBH4 solution. The solutions were mixed via vigorous stirring for 1 h. The gold colloids were red-brown and showed two visible absorption bands at 218 nm and 530 nm (Figure S1). (b) In the second method, the gold colloids were prepared by the method described by Lee and Meisel.21 71 μl of 1 M HAuCl was dissolved in 50 mL of water and the solution was brought to boiling. A solution of 5 mL sodium citrate (1 wt %) was added. Boiling was continued for ca. 1 h. The gold colloids were purple and had absorption maxima at approximately 525 nm (Figure S1). SERS measurements For SERS measurements, conjugation of cysteine and gold nanoparticles was formed by mixing 100 µL gold colloid solutions with 100 µL of 2 x 10-4 M cysteine solutions. The pH values of 10-4 M cysteine in these two kinds of gold colloids were about 6.0 in this work. 5 µL of the mixture was deposited into the groove of a quartz slide. All the Raman spectra with resolution ca. 3 cm-1 were recorded using XploRA Raman spectrometer (HORIBA JOBIN YVON). The SERS spectra of the mixture of cysteine and Au colloids ware measured by using a 785 nm laser. The laser power at the sample was ca. 1.2 mW while the exposure time was typically 10 s. The spectra were measured with at least 3 repeats. The SERS spectra of cysteine and gold nanoparticles reduced by (a) sodium borohydride and (b) sodium citrate are shown in Figure S2, respectively, and these two SERS spectral patterns are similar. The SERS spectra which show the main characteristic bands agree with the previous SERS experiments on cysteine in gold colloids (Figure 7c of Ref 11)11, as well as the SERS spectra of the mixture of cysteine and gold colloids (Figure 3a of Ref 10).10 The experimental SERS spectra of cysteine in different gold colloids under different preparation conditions are very similar, indicating that cysteine should be adsorbed on the surface of different gold colloids with the same adsorption conformation. In this work the spectra from gold colloids reduced by sodium borohydride are comparable with the simulated spectra. Characterization of gold nanoparticles after the adsorption of cysteine. To figure out the nanostructure and morphology of gold colloids reduced by NaBH4 after the adsorption of 10-4 M cysteine, transmission electron microscope (TEM) imaging and energy-dispersive X-ray spectroscopy (EDS) mapping were performed on a Talos F200X microscope operated at an accelerating voltage of 200 kV, as shown in Figure 2. The average particle size of the gold colloids was about 20-40 nm, and they aggregated due to the adsorption of cysteine. The spatial distribution of S and N coincides with the spatial distribution of the gold nanoparticles, indicating that cysteine has been adsorbed on the nanoparticles.


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Figure 2 (a) TEM images of gold colloids after the adsorption of 10-4 M cysteine. (b, c, d) The area distribution of Au (yellow), S (blue) and N (green), respectively. (e) EDS spectra of gold colloids after the adsorption of 10-4 M cysteine.

Computational Details DFT calculations were carried out using Gaussian 09 software.22 The calculations in this work were performed by applying the functionals DFT-D3 correction versions of M06-2X unless noted otherwise.23-24 The M06-2X (hybrid meta-GGA exchange-correlation functional) is a high-nonlocality functional with double the amount of nonlocal exchange (2X) for nonmetals. Corminboeuf et al. had demonstrated that standard density functionals failed to accurately describe interaction energies of charge-transfer complexes not only because of the missing long-range exchange as generally assumed but also as a result of the neglect of weak interactions.25 However, these could be properly described when using well-balanced functionals such as PBE0-dDsC, M06-2X, and LC-BOP-LRD.25 The method of dispersion correction (DFT-D) as an add-on to standard Kohn–Sham density functional theory has been refined regarding higher accuracy, broader range of applicability, and less empiricism.26 The new DFT-D3 versions have been thoroughly tested not only on common organic and noncovalently bound complexes, but also on large, infinite, “heavy”, and metallic systems. DFT-D3 performs high accuracy for dispersion corrections and superior for thermochemical, intramolecular dispersion effects.26 Grimme et al. had made a thorough benchmark of density functional methods for general main group thermo-chemistry, kinetics, and noncovalent interactions, and found that M062X-D3 could be statistically the best of all 23 hybrids-level functional.27 And in our previous work,28 we had showed that the Raman spectra and the geometry parameters of the amino acid molecules (p-tyrosine, m-tyrosine) could be best described by M06-2X-D3 functionals. The basis set used for C, N, S, O, H atoms in this work was the 6-311++G(d,p), which are suitable for amino acids.28-29 The pseudopotential basis sets LANL2DZ was used for the Au atoms. The tight convergence criterion of Gaussian 09 was used in structure optimization, and the ultrafine integration grid was used in the numerical integration of the structure optimization and vibrational frequencies calculation. The geometries of cysteine-Aun complexes were fully optimized without any



constraint on the geometry and the optimized structures had no imaginary frequencies. The calculations of the harmonic vibrational wavenumbers and relative Raman activities were carried out at the same level of theory using the same basis sets. The scaling factor for the harmonic vibration frequencies of M06-2X-D3/6–311++G(d,p)/LANL2DZ was 0.983.30-31 Then the calculated activities were converted using the following relationship derived from the basic theory of Raman scattering:32-33 = − ⁄ 1 − −ℎ ⁄ , where is the exciting frequency (in unit of cm-1), is the vibrational frequency (in unit of cm-1) of the ith normal mode, h, c, and k are fundamental constants, and f is a suitably chosen common normalization factor for all peak intensities. Relative multiples of the spectral intensity ranges are marked on the right Y axis as X1, X2, X5, et al. The Raman spectra shown in this work have a Lorentzian line width of 8 cm−1. Vibrational frequency assignments were made based on the results of the Gaussview program 5.0.8 version,34 and the potential energy distribution (PED) matrix was expressed in terms of a combination of local symmetry and internal coordinates. In the calculation work, we studied the zwitterionic forms of cysteine, because the pH value of 10-4 M cysteine in the gold colloids was about 6.0 in this work. The pKa value of the carboxyl group in cysteine was 1.9, therefore, the carboxyl group was expected to be unprotonated and the amino group is at the protonated form under the conditions used to record SERS spectrum.10, 35 It was also reported that cysteine was usually in zwitterionic form in solution, such as cysteine deposited from an aqueous solution formed a ordered film on the Au (111) surface.36 The implicit solvent models SMD under default setting in Gaussian 09 package were employed for the calculations of both the energy and vibrational properties.37 Besides, the influence of explicit one and more water molecules on the Raman spectra is shown the Figure S3. Since the Raman spectra are only slightly changed, the implicit solvent models are therefore enough accurate for us to simulate and interpret the Raman spectra in this work.

Results and Discussion 1. Conformers of cysteine-gold cluster complexes From the SERS spectra of cysteine on gold colloids (Figure S2), the absence of the band at about 490 cm-1 from the stretching vibration of S-S band of cystine (cys-cys dimer)11 indicates that cysteine was not aggregated. Therefore, we considered that the cysteine monomer was adsorbed on the gold nanoparticles.11 The cysteine molecule is usually adsorbed on gold by its sulfur atom, after cleavage of the S-H bond with its deposition from aqueous solution to the metal surface.17, 38-39 The absence of the S-H stretching vibration band in the SERS spectra (Figure S2) which should appear at about 2570 cm-1 in the ordinary Raman spectrum of cysteine surmises that the thiol was ionized at the metal surface.10-11, 38 Further evidence for the gold-sulfur interaction comes from the formation of the Au-S vibrational band at 267 cm-1 (Figure 3a of Ref. 10) of SERS spectra of cysteine on the gold colloids.10 Besides, Cavalleri et al. have investigated the electronic states of cysteine adsorbed on Au (111) from aqueous solution with synchrotron-based, high resolution X-ray photoemission spectroscopy.39 The analysis of the S 2p core level region in pristine samples prepared with purified cysteine indicates that cysteine is adsorbed onto gold through thiolate.39 The 1H NMR spectrum in aqueous solution also demonstrates that the sulfide bond of cysteine interacts with colloidal gold nanoparticles surface.40


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In our simulation of cysteine-Aun models, the initial structures were constructed by cysteine adsorbed to the Aun cluster by the combination of the possible bonds S-Au, -CγO2--Au, and -NH3+-Au. But there are no stable structures that could be optimized in which the -NH3+ group is close to the Aun cluster. This means that the cysteine may not be adsorbed to the gold substrate through -NH3+group under normal conditions. This is also proved by the polarization-dependent SERS study of cysteine on the gold films.41 Since vibrational modes associated with functional groups lying closer to the surface of the metal and having polarizability components perpendicular to the surface will display a stronger polarization effect, hence, this result suggests that cysteine was adsorbed and had a preferred orientation with respect to the surface (i.e., it had bound to the gold by its thiol group and its carboxylic acid group).41 Therefore, the cysteine-Aun models were constructed by the possible bonds S-Au, -CγO2--Au in this work. Previous research results showed that the sulfur atom is connected to Au atom, but whether O atom is connected to Au atom has not been determined. In this work four gold atoms as a cluster simulated the SERS substrate, which had been successfully applied in DFT simulation of SERS of some molecules.13, 42 Since cysteine has three isomers of different rotable χ1(S-Cβ-Cα-Cγ) torsional angle,2, 10, 43 when cysteine is adsorbed on metal surface, the conformers with different torsion angles may also exist.2, 6 Based on the denotation of references 6 and 10, there are three possible rotational conformers of cysteine that may be stabilized by interaction with the metal surface.6 As shown in Figure 1 and 3, PH/PN/PC series refer to the conformers constructed with H atom/NH3+ group/ CγO2- group in the para-position of the S atom, respectively. For instance, the PH/gauche means both CγO2- and NH3+ on the gauche position. The PN/anti(I) is constructed with an anti-position for the NH3+ and a gauche position for the CγO2-. The PC/anti (II) is constructed with a gauche position for the NH3+ and an anti-position for the CγO2-. PH/PN/PC denote the free cysteine conformers which are not interacting with gold. The structures and Raman spectra of the free cysteine conformers (PH, PN, PC) calculated at the same level of theory are shown in Figure S4. In this work, the cases for cysteine adsorbed to the gold cluster through none, one or two oxygen atoms in adding to sulfur atom were also considered. In the case of cysteine adsorbed on gold only through sulfur atom, O0 denoted the case with none oxygen atom adsorbed, and the three conformers PHO0, PNO0, PCO0 are shown in Figure 3A. In the case of sulfur atom and only one oxygen atom was adsorbed, one oxygen atom was closer to the NH3+ group, and the other oxygen was closer to the H atom. As shown in Figure 3B, ON denotes that the Au atom is connect with the oxygen close to the NH3+ group, while OH denotes that the Au atom is connected with the oxygen close to the H atom. Therefore, six different isomers are defined in Figure 3B, as PNON, PNOH, PCON, PCOH,PHON and PHOH. The charges of these 9 complexes are 0 and spin multiplicities are 2, and the optimized structures are shown in Figure 3A and 3B. In the case of two oxygen atoms are adsorbed, as shown in Figure 3C, PHO2 means that the gauche/PH both the CγO2- and NH3+ are on the gauche position and two oxygen atoms are both adsorbed to the gold clusters, also similarly for PNO2 and PCO2. The charges of these PHO2 and PNO2 complexes are +2, and the spin multiplicities are 2. The charge of the PCO2 complex is +3, and the spin multiplicity is 1. The optimized structures are shown in Figure 3C. In the PCO2 complex, due to the distance between the sulfur atom and the CγO2- group, a cluster of at least six gold atoms is required to simulate the metal substrate. The charges, spin multiplicities and some important geometric parameters of these 12 complexes as shown in Figure 3 are listed in Table S1. The 9 complexes in Figure 3A and



3B have the same charge, spin multiplicity with the gold cluster, therefore, the relative energies and the binding energies of these 9 complexes are also calculated and listed in Table S2. The complexes PHO0/PNO0/PCO0 which are bound to the gold cluster only by the S-Au bonds, and they are less stable than the complexes which are bound to the gold cluster by the S-Au and O-Au bonds. The PHOH and PHON complexes are most stable in the view of energetics, and the energy of complex PCOH is the third most stable in the 9 complexes, only 2.89 kcal/mol higher than PHOH. The binding energies of these complexes are about 30 to 40 kcal/mol, confirming that cysteine can be chemically adsorbed to the gold surface.

Figure 3 The optimized structures of conformers of cysteine bonding with the gold cluster through (A) sulfur atom (B1, B2) sulfur atom and one oxygen atom (C) sulfur atom and two oxygen atoms 2. Raman spectra of conformers The simulated Raman spectra of 12 complexes and experimental spectra are shown in Figures 4, 5 and 6. The frequencies of the vibrational modes of 12 complexes are also given (Table S3 in Supporting Information), and the frequencies of PH, PN and PC conformers of free cysteine can thus be compared therein. Generally, the wavenumbers of bands are shifted in varying degrees for different complexes due to the influence of the chemical interaction with gold clusters. The strong band of free cysteine conformers at about 2690 cm-1 is from the stretching vibration of S-H bond (thiol group), and the weak band at about 980 cm-1 is from the bending vibration of thiol group. In the Raman spectra of the cysteine-Aun complexes, these two bands disappear due to the formation of S-Au bonds instead. Besides, the bands in the region of 600 – 1000 cm-1 are


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shifted considerably when cyseine interacts with gold. Because these bands of free cysteine contain more or less a part of stretching vibration of C-S bond or a part of bending vibration of C-S-H, although the bands are shifted with interaction with gold, some characteristic bands of free cysteine conformers can still be identified, while the frequency shift or difference can help to determine the rotamers. For instance, PH serial conformers (PH, PHO0, PHOH, PHON, PHO2) have a medium intensity band at about 460 - 480 cm-1, but none for PC and PN serial conformers. For the PN serial conformers (PN, PNO0, PNOH, PNON, PNO2), the bands from stretching vibration of Cβ-S bond are all located at about 750 - 770 cm-1, while the bands at located at about 680 - 710 cm-1 for PC and PH serial conformers. In the experimental spectra, the band at 673 cm-1 is rather intensive, while only the spectra of PHON, PHOH, PCOH and PHO0 can reproduce the intensity and wavenumber of this band. We found that the spectra of PNOH, PCON, PNO0, PCO0, PHO2, and PNO2 cannot reproduce intensity of this band, and the wavenumbers of the band of PNON and PCO2 are not very consistent with the experiment. There are two strong bands at about 900 cm-1 and 1050 cm-1, and some weaker bands in the regions between 700 cm-1 to 1250 cm-1. Only the results of PCOH, PCON, PNOH and PCO2 can reproduce the wavenumbers and intensities of these two strong bands. Only PCOH has three strong bands at about 1292 cm-1, 1339 cm-1 and 1391 cm-1 in the regions between 1250 cm-1 to 1500 cm-1, but the simulated wavenumbers are overestimated. Owing to the universally used frequency scaling factor, the wavenumber values of bands below 1250 cm-1 can be corrected, but the corrected wavenumbers of bands over 1250 cm-1 are usually a little overestimated when compared with the experimental values.42, 44-45 With comparison and analysis of the theoretical and experimental data, the Raman spectra of PCOH complex (Figure 5) can mostly reproduce the measured SERS spectra for gold colloids (Figure 5). We have therefore figured out the most dominant adsorption configuration for cysteine attached on the surfaces of gold nanoparticles, in which cysteine interacts with Au cluster through both S and O sites, and cysteine forms a gauche position for the NH3+ and an anti-position for the CγO2-. On the other hand, the effect of the level of theory was also checked, and the other two well evaluated functionals,27 namely, DFT-D3 correction versions of B3LYP and DFT-D correction of ωB97X-D, were employed to simulated the Raman spectra of a series of complexes (PHON, PHOH, PNON, PNOH, PCON and PCOH) and the results are shown in Figure S6 and S7, respectively. Similarly, the Raman spectra of PCOH complex (Figures S6 and S7) can mostly reproduce the measured SERS spectra for gold colloids. Their frequencies of the vibrational modes are also listed in the Table S4 in Supporting Information. The standard deviations of the same vibrational mode calculated by these three functionals are rather small (5 cm-1 on the average), indicating that the Raman spectra simulated by M06-2X-D3 in this work are credible.



Figure 4 The experimental SERS spectra of 10-4 M cysteine in gold colloids (blue line), and the DFT-simulated Raman spectra of the three conformers of cysteine bonding with the gold cluster through sulfur atom (black lines). Multi.: spin multiplicity.


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Figure 5 The experimental SERS spectra of 10-4 M cysteine in gold colloids (blue line), and the DFT-simulated Raman spectra of the six conformers of cysteine bonding with the gold cluster through sulfur atom and one oxygen atom (black lines).



Figure 6 The experimental SERS spectra of 10-4 M cysteine in gold colloids (blue line), and the DFT-simulated Raman spectra of the three conformers of cysteine bonding with the gold cluster through sulfur atom and two oxygen atoms (black lines). In order to verify the reliability of adsorption on PCOH conformers, cysteine absorbed to six different gold clusters were simulated and the result are shown in Figure 7. The Raman spectra, the charges and the spin multiplicities of the whole molecule-cluster systems and the optimized structures are shown in the figure, and the vibrational frequencies are also listed in Table S5. The XPS measurements by Pagliai et al. showed that in the silver and gold colloids, both silver and gold surfaces presented a sizable amount of metal atoms with oxidation number +1, which allows the metal cluster take zero, one, or even more positive charges.12 From comparison of Figure 7a with Figure 7b, Figure 7c with Figure 7d, we see that the difference of the charge mainly influence the structure of the metal clusters, but do not obviously influence the chemical interaction between cysteine and metal cluster. When cysteine molecule is absorbed to significantly different clusters (Figure 7a to Figure 7f), the structures of the cysteine would have only slight differences. And the differences between the Cγ-O-Au and Cβ-S-Au angles of these structures do not exceed 10 degrees, respectively. The difference between the bond lengths of O-Au and S-Au bonds does not exceed 0.1 Å. Therefore, it’s reasonable that the simulated Raman spectra of these conformers have the similar the Raman shifts and relative intensities. The standard deviations of the same vibrational modes of the complexes with different gold clusters are less than 10 cm-1 (4 cm-1 on the average), as shown in Table S5. Therefore, the structures of


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gold clusters may have little influence on the Raman spectra when cysteine interacts with the substrate through the same sites. Thus the metal cluster with four atoms may be enough for the simulation of the Raman spectra of cysteine on the gold surface. This agrees with Wu et al that the size of the silver cluster does not influence significantly the Raman spectra of adsorbed adenine.13 Since gold atoms on the gold colloid surfaces are not periodically regular, the spatial structure of gold atoms on the surface is different, similar to the different spatial structure of the simulated clusters. These can induce small difference of structural parameters of cysteine on the gold surfaces and the small Raman shifts of bands, which may explain that the widths of experimental SERS bands are rather wide.

Figure 7 The experimental SERS spectra of 10-4 M cysteine in gold colloids (blue line), and the DFT-simulated Raman spectra of the six PCOH conformers with different gold clusters (black lines).



3. Vibrational assignments A vibrational normal-mode analysis of L-cysteine has been carried out.46 According to the calculations, Raman frequencies can be used to identify specific rotamers of cysteine in solution.46 Unfortunately, the conformation-sensitive modes are the Cβ-S stretch and the S-H stretch. The oxidative adsorption of cysteine on gold breaks the S-H bond, and the Cβ-S mode is also strongly perturbed by the presence of the surface. The adsorption behaviors of cysteine in gold colloidal solution was resulted from the ‘‘surface selection rules’’ and may be not credible enough.10-11 Many previous works 10-11 generally surmised the vibrational modes of cysteine adsorbed on the gold surface without consideration the chemical interaction of metal clusters with cysteine. As seen in Figure 4, 5, 6, Figure S4 and Table S3, the wavenumbers of the bands are shifted in varying degrees for different complexes due to the influence of the chemical interaction with gold clusters. For instance, the wavenumbers of CγO2- symmetric stretching vibration of free cysteine (PH, PN, PC in Figure S4) are 1408 cm-1, 1419 cm-1 and 1412 cm-1, respectively. These bands shift only a small amount when the cysteine interacts with gold cluster not through the oxygen atom, which are 1417 cm-1 for PHO0, 1413 cm-1 for PNO0 1417 cm-1 for PCO0 while the intensities of these bands are weak. However, when the cysteine interacts with gold clusters through one or two oxygen atom, these bands are moved to 1411 cm-1 for PHON, 1420 cm-1 for PHOH, 1402 cm-1 for PNON, 1420 cm-1 for PNOH, 1370 cm-1 for PCON, 1368 cm-1 for PCOH (Figure 5), 1436 cm-1 for PHO2, 1432 cm-1 for PHO2, 1428 cm-1 for PCO2 (Figure 6), respectively. To be noted, the intensities of these bands are all rather strong. The vibrational modes of the cysteine-gold cluster complex (PCOH) are assigned in Table 1. The strongest Raman band observed at 673 cm−1 is assigned to stretching vibration of Cβ-S bond, combining with the scissoring vibration of CγO2-, same as almost all previous literatures. For the PN serial conformers (PN, PNO0, PNOH, PNON, PNO2), the simulated SERS bands of stretching vibration of Cβ-S bond are all located at about 760 cm-1. For PC serial conformers and PH serial conformers, the bands are at about 680 to 700 cm-1 region, meaning that the major χ1 rotamers may be not only in PH type,10-11 but also in PC type. Besides, in the simulated Raman spectra of free cysteine (Figure S4), this band of both PH and PC rotamers is also at about 685 cm-1. Therefore, in Ref. 10 and 11, it was not rigorous to judge that cysteine is adsorbed to the surface of gold in PH serial conformers only according to the information of this band.10-11 So we adopted additional ways, and in the simulated Raman spectra of PH serial conformers (PHO0, PHOH, PHON, PHO2 and PH), they all have a medium intensity band at about 465 cm-1 which is assigned to the out-of-plane bending of CγO2-, combining with the bending of Cα-Cβ-N. This band cannot be observed on the experimental SERS spectrum, which also indicates that cysteine is not adsorbed as the PH series conformers. The 1339 cm-1 band is mainly assigned to the CγO2- symmetric stretching vibration combining with the bending vibration of Cα-H, and the wavenumber of this band is reduced from the normal Raman band of CγO2- symmetric stretching at about 1400 cm-1, maybe caused by the chemical interaction between the oxygen atom and gold substrate.11 The band at 900 cm-1 is mainly assigned to the Cα–Cγ stretching vibration combining with the rocking the NH3+ group and scissoring of the CγO2- group.10-11, 28, 47 The enhanced of this band may also be caused by the chemical interaction between the oxygen atom and gold substrate. In the simulated Raman


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spectra of PN serial conformers (PNON, PNOH, PNO0, PNO2) and PH serial conformers (PHON, PHOH, PHO0, PHO2), the bands from Cα–Cγ stretching vibration are located at about 850 cm-1. This means that the major χ1 rotamers may be not in PN and PH type. In the previous work,10-11 based on the observation that these bands involving the vibrational motions around Cα−N were enhanced, researchers deduced that the cysteine interaction with Au NPs might preferentially occur also through NH3+ terminal groups. But the bands at the 1500-1600 cm-1 region are also from the terminal groups. If the NH3+ terminal is close to the Au clusters (such as PCO2, PHO0), the simulated Raman bands at the 1500-1600 cm-1 region are very strong. But in the experimental SERS spectra, the bands at the 1500-1600 cm-1 region are very weak. This means that the cysteine interaction with Au NPs may not be through NH3+ terminal groups. The band at 1050 cm-1 is assigned to twisting vibration of CβH2 and the stretching vibration of Cα−N.11 The 1292 cm-1 band is assigned to the bending of Cα-H and wagging of CβH2. The 1391 cm-1 band is mainly assigned to scissoring of CβH2. The intensities of these bands in the simulated Raman spectra of different conformers are all not low. And the simulated wavenumbers from the same vibrational mode of different conformers are close to each other. For example, the simulated bands from twisting vibration of CβH2 of all conformers (PN, PH, PC serial conformers) are all at 1060-1070 cm-1 region. This may be due to the fact that the vibration of CβH2 group is not insensitive to χ1 rotating isomers and the CβH2 group does not directly contact with the substrate.



Table 1. Comparison between the SERS spectra and theoretically calculated spectra of cysteine in Au colloids, the assignments and PED of vibrational modes of PCOH complex at M06-2X-D3/6-311++G(d, p) (C, N, O, S and H) level/LANL2DZ (Au) level. exp

a

1574

exp

b

1571

exp

11

--

exp

10

1599

cal

PED(%)

1584

asym str CγO2- (50), bend NH3+ (25)

1576

bend NH3+ (78), asym str CγO2- (10)

1560

bend NH3+ (72), asym str CγO2- (14)

1448

sym bend NH3+ (81)

1444

bend Cα-H(35), sym str CγO2- (15), sicss CβH2(14)

1391

1391

1392

--

1436

sicss CβH2(46)

1339

1339

1343

1337

1368

sym str CγO2- (37), bend Cα-H (34)

1292

1290

1295

1295

1313

bend Cα-H (27), wag CβH2(26)

1232

1240

--

--

1254

twist CβH2(52)

1228

wag CβH2(31), bend Cα-H (18)

1128

str Cα-Cβ(36), rock NH3+(15), str Cα-N(12)

1072

rock NH3+(40)

1125

1125

--

--

1050

1050

1048

1058

1063

twist CβH2(37), str Cα-N(24)

949

953

--

--

949

str Cα-Cβ(34), rock NH3+(26)

900

899

900

907

889

str Cα-Cγ(21), rockNH3+(14), sciss CγO2-(12)

832

838

--

832

834

wag CβH2(38), str Cα-N(23)

789

790

--

--

807

bend CγCαCβ(36), str Cα-S(21), str Cα-Cβ(11)

684

str Cβ-S(51), sciss CγO2-(25)

679

str Cβ-S(30), sciss CγO2-(23), bend-out CγO2-(19)

535

bend CαCγO(37),bend-out CγCαCβ(19), str Cα-N(15)

673

671

527

524

665

672

The wavenumbers of experimental SERS spectra of cysteine on gold nanoparticles reduced by (a) sodium borohydride and (b) sodium citrate in this work, (11) sodium citrate in Ref. 11, (10) sodium citrate in Ref. 10. Bend, bending; bend-out, out of plane bending; rock, rocking; sciss, scissoring; str, stretching; twist, twisting; wag, wagging; asym, asymmetry; sym, symmetry.


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Conclusion The paper reports the study of the adsorption behavior of L-cysteine on gold nanoparticles through the methods of experiment SERS and theoretical DFT simulation. DFT method was used to construct a series of conformations of rotational isomers and different adsorption sites so as to simulate the corresponding Raman spectra. Through comparison of spectral profiles of the experimental with the calculated Raman spectra, we found that the adsorption of cysteine on the surfaces gold nanoparticles adopted the most predominant adsorption configuration in which cysteine chemically interacts with Au cluster through both S and O sites, and cysteine forms the configuration with a gauche position for the NH3+ and an anti-position for the CγO2-. Furthermore, we also demonstrated that the method applied in this work may also be useful to study the adsorption of other amino acids on the surface of metal nanoparticles.

Supporting Information Description Figure S1. UV-visible absorption spectra of prepared gold colloids: (a) reduced by sodium borohydride; (b) reduced by sodium citrate. Figure S2. SERS spectra of cysteine adsorbed on the prepared gold colloids: (a) reduced by sodium borohydride; (b) reduced by sodium citrate. Figure S3. DFT-simulated Raman spectra of the PCOH conformers with (a) three, (b) two, (c) one and (d) none water molecules. Figure S4. Optimized structures and simulated Raman spectra of the PH, PN and PC conformers of free cysteine which are not interacting with gold at M06-2X-D3/6-311++G(d, p) (C, N, O, S and H) level. Figure S5. blue line: the experimental SERS spectra of 10-4 M cysteine in gold colloids. Black lines: the DFT-simulated Raman spectra of the six conformers of cysteine bonding with the gold cluster through sulfur atom and one oxygen atom at B3LYP-D3/6-311++G(d, p) (C, N, O, S and H) level/LANL2DZ (Au) level. The scaling factor for the vibrational frequencies is 1.0008. Figure S6. blue line: the experimental SERS spectra of 10-4 M cysteine in gold colloids. Black lines: the DFT-simulated Raman spectra of the six conformers of cysteine bonding with the gold cluster through sulfur atom and one oxygen atom at ωB97X-D/6-311++G(d, p) (C, N, O, S and H) level/LANL2DZ (Au) level. The scaling factor for the vibrational frequencies is 0.9867. Table S1. Charges, spin multiplicities and some important structural parameters of the 12 different complexes optimized at M06-2X-D3/6-311++G(d, p) (C, N, O, S and H) level/LANL2DZ (Au) level. The bond lengths (unit in angstroms, Å), the angles and dihedral angle (unit in °). Table S2. The relative energies (in kcal/mol) of different cys-Au4 complexes and the binding energy (in kcal/mol) of different cys-Au4 complexes calculated at M06-2X-D3/6-311++G(d, p) (C, N, O, S and H) level/LANL2DZ (Au) level. The Basis Set Superposition Error (BSSE) has been taken into account in the calculations of the binding energies. Table S3. The vibrational frequencies (cm-1) of the calculated Raman spectra of 3 cysteine conformers (PH, PN and PC) which are calculated at M06-2X-D3/6-311++G(d, p) (C, N, O, S and H) level and 12 cysteine-Aun complexes which are calculated at M06-2X-D3/6-311++G(d, p) (C, N, O, S and H) level/LANL2DZ (Au) level. Table S4a&S4b. The vibrational frequencies (cm-1) of the calculated Raman spectra of complexes (PHON, PHOH, PNON, PNOH, PCON and PCOH) which are calculated using the M062X-D3, B3LYP-D3,



ωB97X-D functionals, and the basis sets are 6-311++G(d,p) for (C, N, S, O and H)/LANL2DZ for (Au). Table S5. The vibrational frequencies (cm-1) of the calculated Raman spectra of PCOH with different Aun clusters which are calculated at the M062X-D3/6-311++G(d,p) (C, N, S, O and H)/LANL2DZ(Au) level.


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Acknowledgements This work was partly supported by the National natural Science Foundation of China (11635013, 11475217, 11775272) and the Anhui Provincial Natural Science Foundation (1508085QB44). The computation work was supported by USTC-SCC Supercomputer Centers.

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DFT and SERS Study of L-Cysteine Adsorption on the Surface of Gold

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