DFT and SERS Study of 15N Full-Labeled Adenine Adsorption on

Article pubs.acs.org/JPCC

DFT and SERS Study of 15N Full-Labeled Adenine Adsorption on Silver and Gold Surfaces Guohua Yao,† Zhimin Zhai,†,‡ Jie Zhong,†,‡ and Qing Huang*,†,‡ †

Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China ‡ University of Science & Technology of China, Hefei, Anhui 230026, PR China S Supporting Information *

ABSTRACT: Adsorption of nucleic acid bases on metal surface of nanoparticles has received much attention recently in bio- and nanotechnology, while it still remains a controversial problem in how adenine is adsorbed onto the metal surface. As the nitrogen in adenine plays an important role in the molecular recognition and interaction, the spectral feature related to the nitrogen is the key to analysis of the adsorption configurations. For this purpose, we employed density functional theory (DFT) calculations at B3LYP/6-311+G(d,p) level for the simulation of adsorption configurations, and in the meantime we checked the corresponding surface enhanced Raman spectroscopy (SERS) of 15N fully labeled adenine adsorbed on the surfaces of silver and gold nanoparticles both experimentally and theoretically. The agreement of spectral positions, intensities, and isotopic shifts of the SERS bands, suggests that adenine adsorbed on either silver or gold surface takes the same adsorption configuration in which N7H adenine interacts with Ag4+/Au4+ cluster through both N3 and N9 sites. This study therefore may not only provide new insight into the interaction of adenine with noble metals but also have demonstrated the effective approach based on the combination of DFT and SERS tools applied in isotopic molecules to the issue of adsorption of nucleic acid bases onto metal surfaces in general.

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INTRODUCTION The phenomenon that nucleic acid bases are adsorbed onto the metal surface of nanoparticles has been well identified and applied in biology and nanotechnology.1 In particular for adenine, since the surface enhanced Raman spectroscopy (SERS) of adenine was first reported by Koglin et al.,2,3 researchers have employed varied techniques to interpret the adsorption configurations, such as SERS, FT-IR, X-ray photo electron spectroscopy (XPS), and scanning tunneling microscopy (STM).4−12 However, many reported results are contradictory with each other as to explain the interaction between adenine and the metal surface. Recently, density functional theory (DFT) computation has been utilized in the research the adenine adsorption modes, which can well reproduce the measured SERS spectra of adenine in silver/gold colloids.5−8 In the reported DFT simulations, the model of molecule−metal cluster complex was assumed with the adenine contacting the metal surface via different nitrogen sites. However, there are still big differences in the opinion on how the adsorption takes place on various metal surfaces. For the interaction of adenine with silver surface, Huang et al. have reached the conclusion that N7H interacts with one positively charged silver cluster via N3 and N9 at the same time.6 However, Lang et al. claimed that adenine interacts with the silver surface via N3 or through N3 and the external amino group.5 For the interaction of adenine with gold surface, Pagliai et al. concluded that adenine © XXXX American Chemical Society

may more likely interact with gold surface via N3, but they were not sure if adenine is in N9H or N7H tautomer.7 Kundu et al. suggested that adenine and its derivatives may bind themselves to the Au surface exclusively at nitrogen N7 with the C6−NH2 bond aligned near the surface normal, while binding at N3 is also possible.8 Since the isotope substitution of atoms always lead to shifts of the Raman/IR bands of corresponding vibrational modes, the isotopic labeling of molecule can thus help to analyze the vibrational modes and structure of molecules effectively. Comparison of the experimentally measured and theoretically predicted isotopic shifts of the Raman/IR bands proved to be a good criterion of the assignment of the observed bands to the calculated normal modes.13 Nowak et al. reported the infrared spectra of matrix-isolated adenine and its 15N isotopomers with 15 N at the N9 or N7 positions and reached the conclusion that the N9H tautomer of adenine strongly dominates in lowtemperature matrices.13 Xue et al. employed the IR spectra of adenine-d3(N‑D) and the SQM force field to acquire the reliable assignments of the IR spectra of adenine.14 As the nitrogen in adenine plays an important role in the molecular recognition of nucleic acid bases and in the interaction between adenine and Received: January 25, 2017 Revised: April 4, 2017 Published: April 19, 2017 A

DOI: 10.1021/acs.jpcc.7b00818 J. Phys. Chem. C XXXX, XXX, XXX−XXX

Article

The Journal of Physical Chemistry C

JOBIN YVON). The mixture of Ade/Ade-15N5 and Ag colloids was measured by using a 532 nm laser, while a 785 nm laser was used for SERS from the Au colloids. 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 and used in this work without baseline correction, curve fitting, or normalization. DFT Calculations. DFT calculations were carried out using Gaussian 09 software.16 All calculations were performed by applying the hybrid of Becke’s nonlocal three parameter exchange and correlation functional and the Lee−Yang−Parr correlation functional (B3LYP). The basis set used for C, N, H atoms in this work is the triple-ζ 6-311+G(d,p) which split valence-shell basis set augmented by d-polarization functions on heavy atoms and p-polarization functions on hydrogen atoms as well as diffuse functions for heavy atoms was used. The pseudopotential basis sets Lanl2DZ was used for the Ag and 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 adenine (Figure 1) and adenine−Ag/Au

metal surfaces, the spectral feature of nitrogen is thus very critical for identifying the most possible adenine adsorption modes. Herein, we employed surface enhanced Raman spectroscopy (SERS) combined with density functional theory (DFT) computation in the study of adenine adsorption configurations on the metal surfaces of silver and gold nanoparticles. In the study, we used 15N fully labeled adenine in order to check the correctness of our spectral interpretation. Deuterium isotopic adenine was not selected in this work since N−D can be partially exchanged to N−H easily and might hinder the analysis of the spectrum. Both the nonisotopic and the 15N fully labeled Raman spectra could be reproduced by our DFT calculations. Since neither normal Raman nor SERS spectra of 15N fully labeled adenine, to the best of our knowledge, had been reported before, it is for the first time that the normal Raman spectra of adenine and 15N fully labeled adenine and their SERS spectra in silver and gold colloids have been measured and explained. Accordingly, a series of complexes in different adsorption configurations have been constructed and compared with the results from the former studies.6,7 By comparison and analysis of theoretical and experimental nonisotopic and 15N fully labeled spectra, we have therefore figured out the most dominant adsorption configuration for adenine attached on the surfaces of silver and gold nanoparticles.

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EXPERIMENTAL SECTION Materials. Adenine was purchased from Sigma-Aldrich. High purity water was used in this work. Adeninehydrochloride-15N5 (C5H515N5·HCl) was purchased from Cambridge Isotope Laboratories, Inc. High isotopic purity (98%) fully 15 N-labeled adenine was used to obtain high-resolution 15N Raman and SERS spectra. Adenine hydrochloride (adenine· HCl) was purchased from Sinopharm Chemcal Reagent Co. Ltd. Sodium hydroxide, 1 M solution in H2O was purchased from J&K Scientific Ltd. Equimolar amount of NaOH was added to neutralize the complexed HCl in adenine-15N5·HCl and adenine·HCl. In this work, the neutralized adenine-15N5· HCl is named as adenine-15N5 or Ade-15N5. Fabrication of Silver and Gold Nanoparticles. The aqueous solution of silver colloids was prepared basically following the method described by Creighton et al.15 Silver colloids were prepared by reduction of 50 mL of 10−3 M AgNO3 with ice-cold 150 mL of 2.0 × 10−3 M NaBH4 solution. The AgNO3 stock was stored under dark condition and used within 1 h of preparation. The solutions were mixed with vigorous stirring for 1 h. The silver colloids were yellow and showed a visible absorption band near 389 nm (Figure S1). The aqueous solution of gold colloids was also prepared basically following the method described by Creighton et al.15 The aqueous solution of gold colloids were also prepared by reduction of 20 mL of 2 × 10−3 M HAuCl4·3H2O with ice-cold 60 mL of 2.0 × 10−3 M NaBH4 solution. The solutions were mixed via vigorous stirring for 1 h. The gold colloids were redbrown and showed two visible absorption bands at 218 and 530 nm (Figure S1). SERS Measurements. For SERS measurements, conjugation of adenine and silver or gold nanoparticles was performed by mixing 100 μL silver colloid solutions with 100 μL of 2 × 10−4 M Ade/Ade-15N5 solutions. A 5 μL sample of the mixture was deposited into the groove of a quartz slide. All the Raman spectra with resolution ca. 3 cm−1 were taken in the 200−3500 cm−1 range using XploRA Raman spectrometer (HORIBA

Figure 1. Optimized structure with some structural parameters of (a) tautomer N9H, (b) complex N7H−N3N9−Ag4+, and (c) complex N7H−N3N9−Au4+. N7H−N3N9−Ag4+ means that the complex is constituted by the adenine tautomer N7H interacting with the cluster (Ag4+) through the nitrogen atoms in position 3 and position 9.

complexes (Figure 1 and Figures S3−S8) were fully optimized without any constraint on the planarity and the optimized geometries have no imaginary frequencies, meanwhile the charges and spin multiplicities are shown in the corresponding figures. The calculations of the harmonic vibrational wavenumbers and relative Raman activities were carried out at the same level of theory using the same basis set. The scaling factor for the harmonic vibration frequencies of B3LYP/6-311+G(d,p) is 0.9688.17 Then the calculated activities were converted to relative Raman intensities the using the following relationship derived from the basic theory of Raman scattering:11,18 Ii = f (vo − vi)4 Ai /vi[1 − exp( −hcvi /kT )]

where ν0 is the exciting frequency (in cm−1 units), νi is the vibrational frequency (in cm−1 units) of the ith normal mode, h, c, and k are fundamental constants, respectively, and f is a suitably chosen common normalization factor for all peak intensities. The Raman spectra obtained in this work have a Lorentzian line width of 8 cm−1. Vibrational frequency assignments were made based on the results of the Gauss view program 5.0.8 version19 and the potential energy distribution (PED) matrix as expressed in terms of a combination of local symmetry and internal coordinates. All B


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Figure 2. Blue lines: the experimental Raman spectra of recrystallized (a) Ade and (c) Ade-15N5. Red lines: the DFT simulated Raman spectra of the tautomer N9H of (b) Ade and (d) Ade-15N5. The charge and spin multiplicity of the molecule are shown on the left of the figure.

shaking for 10 min. The Raman spectra of 10−3 M neutralized adenine·HCl and normal adenine are almost the same (Figure S2), proving that the complexed HCl has been removed from adenine·HCl. The shapes of theoretical spectrum can well conform to experiment, but the wavenumbers are underestimated by about 15 cm−1. Since the used vibrational frequency scaling factor is universal for molecules in general, there may be a small deviation for adenine. The DFT predicted spectrum of adenine agrees well with the experimental normal Raman spectrum (NRS) of polycrystalline adenine (Figure 2). Although the relative intensities are not precisely predicted for all the Raman bands, they are still fairly useful for the assignments of the normal modes in the Raman spectrum. Many DFT studies have provided detailed assignments of nonlabeled adenine and D3-labeled adenine, based on matrixisolated IR spectra, IR−UV ion-dip spectroscopy and Raman spectra of adenine in gas and solid phases and in solution.12,14,20−22 But the vibrational analysis considering 15 N5 fully labeled adenine has not been reported. Figure 2 shows that the experimental spectra of Ade and Ade-15N5 are very similar in their shapes, and the calculated spectra are also very similar. For Ade-15N5, the experimental spectral positions of the Raman bands differ from Ade by red-shift about 11 to 26 cm−1, while the relative calculated bands red-shift about 6 to 21 cm−1. The assignments based on the calculated frequencies and

the normal Raman and SERS bands were assigned to normal modes on the basis of DFT calculations and isotope shifts. It should be noted that the calculated wavenumber values for adenine in the 1100−1700 cm−1 region are overestimated by 2−4%, and there is less deviation below 1100 cm−1.4 Therefore, in this work, owing to the universally used frequency scaling factor 0.9688, the wavenumber values of bands in the 1100− 1700 cm−1 region can be corrected, but the corrected wavenumbers of bands below 1100 cm−1 are usually a little underestimated when compared with experimental values.

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RESULTS AND DISCUSSION Normal Raman Spectra of Adenine and Adenine-15N5. N9H tautomer was found to be the dominant structure of adenine in room temperature as derived from the NMR, Raman, IR studies. 20−22 Thus, the structure and the corresponding normal Raman spectrum of N9H tautomer of Ade and Ade-15N5 was simulated and compared with the experimental spectra. The optimized structure and the number labels of atoms are show in Figure 1, and the Raman spectra are shown in Figure 2, whereas the wavenumbers, Raman shifts caused by 15N labeling, PED and the assignments are listed in Table 1. In the Raman measurement, 200 mL of 10−3 M neutralized adenine was obtained by mixing 100 mL of 2 × 10−3 M adenine·HCl with 100 mL of 2 × 10−3 M NaOH and C


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Table 1. Comparison between the Normal Raman Spectra and Theoretically Calculated Spectra of Ade and Ade-15N5, Raman Shifts Caused by Isotope Labeling, and the Assignments and PED of Vibrational Modes at the B3LYP/6-311+G(d,p) Level expt 1596 1480 1417 1368 1331 1306 1246 1157 1123 1024 939 896

722

619

534

319

Raman shifta

Ade-15N5

adenine calcd 1606 1584 1558 1467 1455 1389 1370 1322 1314 1286 1228 1203 1107 1046 979 946 916 872 825 784 703 664 646 600 557 520 516 504 499 289 268

expt 1583 1464 1403 1357 1305 1285 1229 1140 1104 1008 913 870

703

603

520

308

calcd 1597 1574 1551 1454 1446 1381 1357 1315 1296 1269 1216 1192 1093 1038 967 946 894 850 824 779 688 661 638 587 551 520 504 497 495 282 263

expt −13 −16 −14 −11 −26 −21 −17 −17 −19 −16 −26 −26

−19

−16

−14

−11

calcd

assignments and PEDb

−9 −11 −7 −13 −10 −8 −14 −7 −18 −16 −12 −12 −14 −8 −12 0 −21 −22 −1 −5 −15 −3 −9 −13 −6 0 −12 −7 −4 −7 −6

sciss NH2(41), str C6−N10(16) str N3−C4(20), N1−C6(15), C2−N3 (10) sciss NH2 (60) str N7−C8 (44),bend C8−H (18) str N1−C6 (23), C6−N10(18), bend C2−H(22) str C4−N9 (28), bend C2−H(14),sciss NH2 (10) bend N9−H(27),C2−H(22),str C8−N9 (11), C4−N9 (14) bend C2−H(20), C8−H(12), str C8−N9 (15),C6−N10(12) str N1−C2 (25), C5−N7 (21) str C2−N3 (34),N1−C2(25) bend C8−H(38) N9−H(10),str N7−C8(17) str C2−N3 (32), rock NH2 (25) str C4−N9(30), bend C8−H(12) str C8−N9(54), bend N9−H(31) rock NH2 (45), str N1−C6(26) wag-out C2−H (86) def R5 (77) def R6 (47),str C5−N7 (10) wag-out C8−H (92) def-out R6 (75) ring breath (61) def-out R5, R6 (89) def-out R5 (70), wag-out C8−H(14) def R6 (50) def R5 (11) def-out R6 (75),wag-out C2−H (12) tors NH2 (85) def-R6 (76) def-R6 (52) wag-out N9−H(82) def-out R6(73) rock C6-NH2 (52)

a

Wavenumber of Ade-15N5 subtract wavenumber of Ade bBend, bending; breath, breathing; def, in-plane deformation; def-out, out of plane deformation, rock, rocking; sciss, scissoring; str, stretching; wag, wagging; R5, five-membered ring; R6, six-membered ring. 15

intensities and their similarity to the experimental observations, as well as on the agreement between the theoretical and experimental isotopic shifts. The assignments of the bands in the spectra are given in Table 1. The analysis of experimental and theoretical 15N5 isotopic Raman shifts can help to assign the vibration modes of these bands. Here we take the assignment of the 1331 cm−1 band (Figure 2c) in the Raman spectrum of nonisotopic adenine as an example, as shown in Figure 2 and Table 1. The 15N5 isotopic Raman shifts of the simulated Raman bands of adenine at 1322 and 1314 cm−1(Figure 2d) are −7 and −18 cm−1, respectively. Since the 15N5 isotopic Raman shift of the 1331 cm−1 band (Figure 2c) is −26 cm−1, it can be determined that this band is from the stretching of N1−C2 and C5−N7 bonds (1314 cm−1 in the theoretical spectrum, Figure 2d) rather than the C2−H and C8−H bending (1322 cm−1 in the theoretical spectrum, Figure 2d), and this assignment conforms to the results in the literature.20,21,23,24 Besides, the 1480 cm−1 band can be assigned to N7−C8 stretching motions mixed with C8−H bending based on the comparisons of isotopic shift and intensity, and this assignment agrees with Nowak et al.,24 but it does not conform to the result of van Zundert et al.21 The assignments of most Raman bands are consistent with the results in the literature,23,24 which are confirmed by the

N5 isotopic Raman spectrum. As shown in Figure 2, the intense bands of Ade at 722, 1246, 1331, and 1480 cm−1 (Figure 2c) are shifted to 703, 1229, 1305, and 1464 cm−1 (Figure 2a) in the Raman spectrum of Ade-15N5, and they mainly correspond to the ring-breathing mode, C8−H bending mixed with N7−C8 stretching motions, N1−C2 stretching mixed with C5−N7 stretching motions, and N7−C8 stretching motions mixed with C8−H bending, respectively (Table 1). The bands and 1357 and 1024 cm−1 are mainly from the motions of N9 atom in N9H tautomer, for which the band at 1357 cm−1 is from the N9−H and C2−H bending mixed with C8−N9 and C4−N9 stretching, and the band at 1024 cm−1 is from C8−N9 stretching mixed with the N9−H bending. Adenine Adsorption on Silver Surface. It has been reported that adenine can be adsorbed on silver surfaces via N1, N3, N7, or N9 in the N9H tautomer or N7H tautomer. Similar to the previous results in the literature,6,7,11,12 we have simulated a series of models of adenine adsorbed on one to four Ag atom clusters, where the clusters are neutral or take one positive charge (Figures S3, S4, and S5) and the structures are optimized without imaginary frequencies. Calculated Raman spectra show that spectral features of the complexes depend greatly on adsorption sites of adenine and present significant differences. The corresponding static Raman spectra of these D


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Table 2. Comparison between the SERS Spectra and Theoretically Calculated Spectra of Ade and Ade-15N5 in Ag Colloids, Raman Shifts Caused by Isotope Labeling, and the Assignments and PED of Vibrational Modes of N7H−N3N9−Ag4+complex at B3LYP/6-311+G(d,p)(C, N, and H) Level/LANL2DZ(Ag) level Ade-15N5

adenine

raman shift

expt

calcd

expt

calcd

expt

calcd

assignments and PED

1645 1576 1550

1624 1581 1551 1487 1457 1419 1367 1339 1315 1302 1231 1194 1131 1088 977 953 940 887 861 765 709 677 618 597 545 535 515 502 479 305 297 209

1628 1564 1539

1613 1575 1540 1478 1449 1404 1358 1324 1298 1292 1217 1184 1118 1076 965 953 920 862 860 760 695 672 613 585 537 526 505 501 475 299 290 207

−17 −12 −11

−11 −7 −12 −10 −9 −15 −10 −16 −16 −11 −14 −10 −13 −13 −12 −1 −20 −24 −1 −5 −15 −6 −5 −12 −8 −9 −10 −1 −4 −6 −7 −2

sciss NH2(36),str C6−N10(16),C5−C6(15) sciss NH2(47),C5−C6(13) str N3−C4(41),N1−C6(17),C4−C5(11) str C8−N9(28),C6−N10(12),bend C8−H(18),sciss NH2(10) bend C2−H(35), str N1−C6(18), C2−N3(11) bend N7−H(36),str N7−C8(23),C6−N10(11) str C4−C5(42), N7−C8(15) str N1−C2(38),C6−N10(12),bend C2−H(20) bend C8−H(23),str C2−N3(18),C8−N9(17),C4−N9(11),C5−N7(10) str N3−C4(28),C4−N9(20),N1−C6(14),bend C2−H(10) str C2−N3(29),C8−N9(18),bend C8−H(24) str C5−N7(23), rock NH2 (16),bend C8−H(16) str N7−C8(54),bend N7−H(17) bend N7−H(24), bend C8−H(12),str C5−N7(15) rock NH2 (42), str N1−C6(26) wag-out C2−H (94) def R5 (70) def R6 (30),str C5−N9 (12) wag-out C8−H (86) def-out R6 (75) ring breath (64) def-out R6 (43), def-out R5 (19) def-out R5 (70) def R6 (60), def R5 (10) def-out R6 (33),def-out R5 (21),wag-out C2−H (15) def-R6 (70) def-R6 (51) sciss C5−C6−N1 tors C6-NH2 (90) wag-out N9−H(89) def-out R5 (36), def-out R6 (27) rock C6-NH2 (57) def-out R5 R6 (56) wag NH2 (15)

1458 1395 1370 1332 1304 1258 1194 1117 1026 960

734 692 626 566

357 326 217

1444 1363 1315 1293 1241 1182 1100 1015 945 899

719 683 614 562

352 312 210

−14 −7 −17 −11 −17 −12 −17 −11 −15

−15 −9 −12 −4

−5 −14 −7

spectrum also agree with Huang et al.6 In the SERS spectrum of Ade on silver colloid (Figure 3c), the most intense bands are 734 and 1332 cm−1, which have been reported in the literature.3−6 The 734 cm−1 band is from ring-breathing mode and shift to 719 cm−1 in the 15N SERS spectrum. The 1332 cm−1 band is from bending of C8−H mixed with stretching vibrations of C2−N3, C8−N9, C4−N9, and C5− N7, and shifts to 1315 cm−1 in the 15N SERS spectrum. It is gratifying that the shoulder bands (Figure 3a) at 1293 and 1363 cm−1 near the intense band 1315 cm−1 can be easily identified in the 15N SERS spectrum. The corresponding 1304 cm−1 shoulder band (Figure 3c) in nonisotopic SERS can be identified by using peak fitting, and this band moved to 1293 cm−1 in the 15N SERS spectrum (Figure 3a), mainly from stretching vibrations of N3−C4,C4-N9 and N1−C6. This 1304 cm−1 shoulder band (Figure 3c) has not been distinguished in the nonisotopic SERS spectra of adenine in the literature.4−6 The 1370 cm−1 band (Figure 3c) is mainly from C4−C5 stretching mixed with a small part of N7−C8 stretching; thus, this band shifts to 1363 cm−1 (Figure 3a) by only 5 cm−1 in 15N SERS. Therefore, due to isotopic effect (which may result in alternation of both Raman shift and intensity), the 15N labeling is helpful for the distinguishing and confirmation of the shoulder bands which are otherwise invisible in the normal

complexes are simulated and compared with experiment. The Raman spectra of N7H−N3N9−Au4+ complex (Figure S3, parts f and f1) can mostly reproduce the measured SERS spectra in silver colloids (Figure S3, parts g and g1), indicating that N7H adenine interacts with one positively charged Ag cluster through both N3 and N9 sites (Figure 1b). This result verifies the adsorption configuration obtained by Huang et al.6 The Raman spectra of N7H−N3N9−Au3+ complex (Figure S3, parts f and f1) and N7H−N3N9−Au2+ (Figure S3, parts d and d1) can also comfortably reproduce the measured SERS spectra, for which N7H adenine interacts with one positively charged Ag cluster through both N3 and N9 sites (Figure 1b). Pagliai et al. have presented electrostatic potential of tautomer N7H, suggesting the possibility of N7H to act as a bidentate ligand which means that N7H interacts with metal surface through both N3 and N9 sites.7 They also performed DFT calculations by modeling of the metal surface as Ag3+ cluster (N7H−N3N9−Ag3+ complex) to verify this possibility. In our work, the SERS spectra of Ade-15N5 on silver colloids confirm that the tautomer N7H interacts with silver surface through both N3 and N9 sites. The assignments of the bands and the Raman shifts caused by isotopic labeling are given in Table 2, while the assignments derived from the analysis of both nonisotopic and 15N labeled E


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Figure 3. Blue lines: the experimental SERS spectra of 10−4 M (a) Ade and (c) Ade-15N5 in silver colloids. Red lines: the DFT-simulated Raman spectra of N7H−N3N9−Ag4+complexes of (b) Ade and (d) Ade-15N5.

nonisotopic Raman spectra. To be noted, in this work, the SERS intensity variations due to the electromagnetic enhancement mechanism was not considered, which however would also determine the observed SERS intensities of adenine. Besides, the bands at 626, 566, 692, and 357 cm−1 are out-ofplane deformation of six-member and five-member rings. The out-of-plane wagging of CH and NH vibrations was too weak to be found out in the experimental SERS spectrum. Adenine Adsorption on Gold Surface. Similar to the treatment of adenine on Ag colloid, we also simulated a series of models of adenine adsorbed Au clusters, as shown in Figures S6, S7, and S8. Both the calculated spectra of Ade and Ade-15N5 with Au clusters are compared, and the simulated Raman spectra of N7H−Au4+ complex (Figure S6 parts f and f1) can also mostly reproduce the measured SERS spectra (Figure S6, parts g and g1), indicating that N7H adenine interacts with Au cluster through both N3 and N9 sites (Figure 1c). In particular, the wavenumbers of the bands are well corresponding to the experimental results, as shown in Table 3. The cluster is constituted by four gold atoms with one positively charged, conforming to the XPS measurements by Pagliai et al., showing that both silver and gold surfaces present a sizable amount of metal atoms with oxidation number +1, which allows modeling of the metal active sites as involving Ag+ or Au+ ions.7 Pagliai et al. have calculated the electrostatic potential for N7H form of adenine, and the N3 and N7 atoms constituting the most

negative part of adenine means that the tautomer N7H can interact with the metal surface through the N3 and N7 atoms.7 Therefore, this complex structure agrees with the analysis of the XPS experiment and the electrostatic potential calculation.7 But Pagliai et al. considered that the adenine/Au(0) complexes could provide for both tautomers N7H and N9H with the nitrogen atom in position 3 linked to Au(0), a better agreement with the observed SERS spectrum than those with Au(I) ion.7 Hence, these four complexes N7H and N9H with the nitrogen atom in position 3 linked to Au (0)/Au(I) were calculated and compared in our work, denoted as N7H−N3− Au, N7H−N3−Au+, N9H−N3−Au, and N9H−N3−Au+ as shown in Figure S6 of the Supporting Information. The band near to 735 cm−1 from the ring breathing mode is very intense in the N7H−N3−Au, N7H−N3−Au+, N9H−N3−Au, and N7H−N3N9−Au4+ complexes. The simulated spectra of these four complexes are obviously better than the other complexes in Figures S7 and S8. For the N7H−N3N9−Au4+ complex, in the 1100−1700 cm−1 region of both nonisotopic and 15N5 labeled spectra (Figure S6, parts f and f1), almost all of the bands are more accurately corresponding to the experimental spectra (Figure S6g and S6g1). And in the 500−1100 cm−1 region, the wavenumbers of N7H−N3N9−Au4+ are a little underestimated, similar to the calculation of adenine and adenine−Ag complex. Since there is less deviation for the calculated wavenumbers below 1100 cm−1, while the applied F


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Table 3. Comparison between the SERS Spectra and Theoretically Calculated Spectra of Ade and Ade-15N5 in Au Colloids, Raman Shifts Caused by Isotope Labeling, and the Assignments and PED of Vibrational Modes of N7H−N3N9−Au4+ complex at B3LYP/6-311+G(d,p) (C, N, and H) Level/LANL2DZ(Au) Level ade-15N5

adenine expt

1553 1450 1398 1379 1341 1315 1230 1184 1141 1082 967 918 867

737 679 626 553

327

calcd 1628 1584 1553 1491 1453 1430 1379 1348 1309 1305 1226 1195 1142 1093 980 956 948 898 867 786 713 682 623 600 546 545 522 516 509 324 303 250

expt

1536 1483 1438 1389 1367 1327 1305 1219 1169 1123 1069 948 902 850

721 670 612 547

325

raman shift calcd 1617 1577 1543 1481 1445 1415 1366 1332 1299 1290 1212 1184 1130 1081 967 955 928 875 866 781 699 676 618 588 537 536 515 513 505 317 297 247

expt

−17 −12 −9 −12 −14 −10 −11 −15 −18 −13 −19 −16 −17

−16 −9 −14 −6

−2

calcd

assignments and PED

−11 −8 −11 −11 −8 −16 −13 −16 −10 −16 −14 −11 −13 −12 −13 −1 −19 −23 −1 −5 −15 −6 −5 −12 −9 −9 −8 −3 −4 −7 −6 −3

sciss NH2(33), str C6−N10(20) sciss NH2(44) str N3−C4(19),N1−C6(15),C5−N7(10) str C8−N9(25),C6−N10(12),bend C8−H(20), sciss NH2(10) bend C2−H(31),str N1−C6(17),C2−N3(11) bend N7−H(35), str C7−N8(26),C6−N10(12) def R5 (24), str C4−C5(23),N1−C2(14) str N1−C2(32),C6−N10(13),bend C2−H(29) str C8−N9(18),C4−N9(18),C2−N3(15),bend C2−H(17) str N3−C4(32),C4−N9(15), N1−C6(12) str C2−N3(32),C8−N9(17) bend C8−H(21) str C5−N7(24),rock NH2(16),bend C8−H(14) str C7−N8(51),bend N7−H(17) bend C8−H(19),N7−H(14),def R5 (24) rock NH2(41), str N1−C6(24) wag-out C2−H(94) def-R5 (62) def-R6 (51) wag-out C8−H(95) def-out R6 (77) ring breath (63) def-out R6 (78) def-out R5 (42),wag-out N7−H(26), C8−H(11) def R6 (42) def R6 (43), str C4−N9(17) def-out R5 R6 (56), wag-out C2−H(14) def R6 (37), str C5−N7(13) tors C6-NH2(76) wag-out N7−H(83) def-R6 (43),def-R5 (24) rock C6-NH2 (56) wag NH2 (78)

bands of adenine in Au and Ag colloids have the comparable isotopic Raman shifts both in experimental and theoretical spectra. For example, in the experimental SERS spectra, the wavenumber of breathing mode of Ade-15N5 on gold (Figure 4a) surface is red-shifted by 16 cm−1 compared with that in the nonisotopic SERS (Figure 4c), as shown in Table 3, while the wavenumber of the breathing mode of Ade-15N5 on silver surface (Figure 3a) is red-shifted by 15 cm−1, as shown in Table 2. In the theoretical spectra, the isotopic Raman shifts of their breathing mode are all red-shifted by 15 cm−1, as shown in Table 2 and 3. While in the region between 1200 and 1350 cm−1, the bands and the profiles of SERS spectra on gold and silver surfaces are obviously different, mainly due to that the 1315 cm−1 band (Figure 4c) is not well enhanced while the 1332 cm−1 band (Figure 3c) of adenine in silver colloid is significantly enhanced. The 1315 cm−1 band (Figure 4c) is attributed to stretching vibration of C8−N9, C4−N9, and C2−N3 bonds mixed with bending of C2−H. And the 1341 cm−1 band is attributed to stretching of N1−C2, C6−N10 bonds mixed with bending of C2−H. The assignments of these two bands agree with the study of the pH-dependent on SERS bands by Kundu et al.8 To the best of our knowledge, many SERS bands of adenine in Au colloids assigned in this work had not been reported by

frequency scaling factor is 0.9688, leading to the underestimation of the corrected wavenumbers in the 500−1100 cm−1 region.4 The N9H−N3−Au complex (Figure S6, parts c and c1) cannot appropriately simulate the bands at 1500−1700 cm−1. The N7H−N3−Au (Figure S6, parts a and a1), N7H− N3−Au+ (Figure S6, parts b and b1) complexes cannot appropriately simulate the wavenumbers of the bands at 1100− 1400 cm−1 region, especially for the 15N5 SERS measurement. Since the similarity of the adsorption configuration of N7H− Au4+and N7H−Ag4+, the isotopic Raman shifts and profile of their SERS spectra were also calculated and compared. In the regions excluding the range from 1200 to 1350 cm−1, the profiles of SERS spectra (Figure 3 and 4) of adenine in Ag and Au colloids are very similar both in profiles and wavenumbers of the bands. The SERS bands of adenine in Au colloids at 553, 626, 737, 967, 1184, 1379, 1398, 1450, 1553 cm−1 (Figure 4c) are corresponding to 566, 626, 734, 960, 1194, 1370,1395, 1458, 1550 cm−1 (Figure 3c) for the SERS of adenine in Ag colloids, respectively. Both the simulated spectra of Ade and Ade-15N5 with Au4+ complex are used to assign the bands of SERS spectrum, and the assignments are given in Table 3. It is not surprising that the assignments of these corresponding bands are almost the same for adenine in Au and Ag colloids, respectively (Table 2 and 3). And the same assigned SERS G


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Figure 4. Blue lines: the experimental SERS spectra of 10−4 M (a) Ade and (c) Ade-15N5 in gold colloids. Red lines: the DFT-simulated Raman spectra of N7H−N3N9Au4+ complexes of (b) Ade and (d) Ade-15N5.

constructed by four atoms with one positively charged can suitably simulate the SERS spectra of molecule adsorbed on the metal surface. Some other structural parameters of the silver and gold complexes were also obtained from this study, such as the bond lengths as given in Figure 1. The Au−N bonds are shorter than Ag−N bonds, and the shape of four Au atoms is closer to the square. Besides, the frontier molecular orbital of these two complexes were simulated as given in Figure S9, showing that the HOMO and LUMO orbitals of them are very similar, so that they may have similar chemical properties and spectral phenomena. The specific influence of charge and spin multiplicity on the calculated Raman spectra feature of adenine−Ag 4 /Au 4 complexes was also considered. When the total charges of these complexes are 0 or +2, the spin multiplicities can be 1, 3, and 5. While the total charges of these complexes are +1, the spin multiplicities can be 2, 4, and 6. In the calculation, the structures of N7H−N3N9−Ag4+ and N7H−N3N9−Au4+ are set as the initial structures, and the optimized structures and corresponding Raman spectra are shown in Figures S10 (Ade− Ag4) and S11 (Ade−Au4). The setting of charge and spin multiplicity obviously affects the spectrum and structure of complex. For adenine−Ag4, we found that the Raman spectra of S10d/S10d1 (charge = 1, spin multiplicity = 2) can mostly reproduce the measured SERS spectra. The Raman spectra of S10e/S10e1 (charge = 1, spin multiplicity = 4) and S10g/S10g1

the use of DFT theoretical calculation. For the SERS of adenine in Au colloids (Figure 4c), the most intense band is the breathing mode at 737 cm−1, while the other bands are not so intensely enhanced and relatively weaker. The bands at 1553 cm−1 is from stretching of N3−C4 bond and N1−C6 bond. The bands at 1450 cm−1 is from bending of C2−H bond, mixed with stretching vibration of N1−C6 and C2−N3 bonds. The 1398 cm−1 band is attributed to bending of N7−H, and stretching of C7−N8 and C6−N10 bonds. The bands at 1184 cm−1 is from the stretching of C5−N7, mixed with rocking NH2 group and bending of C8−H. The 967 cm−1 band is from rocking of NH2 group and stretching of N1−C6 bond. The bands at 626 and 553 cm−1 are mainly from out-of-plane deformation of 5 member ring and 6 member ring, respectively. It is noteworthy that the weak band at 1483 cm−1 (Figure 4a) can be identified in the 15N5 SERS, and it is mainly from stretching of C8−N9, C6−N10 bonds and bending of C8−H. This weak band cannot be easily identified in the nonisotopic SERS spectra on Ag and Au colloids. Since the assignments of these corresponding bands of adenine adsorption in silver and gold colloids are nearly the same, respectively, and the N3, N7, and N9 atoms are normally involved in the vibrational modes of these bands, we are therefore ensured that adenine is adsorbed on the silver and gold surface in the same configuration in which N7H adenine interacts with Ag/Au cluster through both N3 and N9 sites. This work thus also proves that the cluster model,6 which is H


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(2) Koglin, E.; Sequaris, J. M.; Valenta, P. Surface Raman-Spectra Of Nucleic-Acid Components Adsorbed at a Silver Electrode. J. Mol. Struct. 1980, 60, 421−425. (3) Ervin, K. M.; Koglin, E.; Sequaris, J. M.; Valenta, P.; Nurnberg, H. W. Surface Enhanced Raman-Spectra Of Nucleic-Acid Components Adsorbed at a Silver Electrode. J. Electroanal. Chem. Interfacial Electrochem. 1980, 114 (2), 179−194. (4) Giese, B.; McNaughton, D. Surface-enhanced Raman spectroscopic and density functional theory study of adenine adsorption to silver surfaces. J. Phys. Chem. B 2002, 106 (1), 101−112. (5) Lang, X. F.; Yin, P. G.; You, T. T.; Jiang, L.; Guo, L. A DFT investigation of surface-enhanced Raman scattering of adenine and 2′deoxyadenosine 5′-monophosphate on Ag20 nanoclusters. ChemPhysChem 2011, 12 (13), 2468−2475. (6) Huang, R.; Yang, H. T.; Cui, L.; Wu, D. Y.; Ren, B.; Tian, Z. Q. Structural and Charge Sensitivity of Surface-Enhanced Raman Spectroscopy of Adenine on Silver Surface: A Quantum Chemical Study. J. Phys. Chem. C 2013, 117 (45), 23730−23737. (7) Pagliai, M.; Caporali, S.; Muniz-Miranda, M.; Pratesi, G.; Schettino, V. SERS, XPS, and DFT Study of Adenine Adsorption on Silver and Gold Surfaces. J. Phys. Chem. Lett. 2012, 3 (2), 242−245. (8) Kundu, J.; Neumann, O.; Janesko, B. G.; Zhang, D.; Lal, S.; Barhoumi, A.; Scuseria, G. E.; Halas, N. J. Adenine- and Adenosine Monophosphate (AMP)-Gold Binding Interactions Studied by Surface-Enhanced Raman and Infrared Spectroscopies. J. Phys. Chem. C 2009, 113 (32), 14390−14397. (9) Vaz-Dominguez, C.; Escudero-Escribano, M.; Cuesta, A.; PrietoDapena, F.; Cerrillos, C.; Rueda, M. Electrochemical STM study of the adsorption of adenine on Au(111) electrodes. Electrochem. Commun. 2013, 35, 61−64. (10) Andrews, K. M.; Pearl, T. P. Modification of Ag(111) surface electronic structure via weak molecular adsorption of adenine measured with low temperature scanning tunneling microscopy and spectroscopy. J. Chem. Phys. 2010, 132 (21), 214701. (11) Muniz-Miranda, M.; Gellini, C.; Pagliai, M.; Innocenti, M.; Salvi, P. R.; Schettino, V. SERS and Computational Studies on MicroRNA Chains Adsorbed on Silver Surfaces. J. Phys. Chem. C 2010, 114 (32), 13730−13735. (12) Huang, R.; Zhao, L. B.; Wu, D. Y.; Tian, Z. Q. Tautomerization, Solvent Effect and Binding Interaction on Vibrational Spectra of Adenine-Ag+ Complexes on Silver Surfaces: A DFT Study. J. Phys. Chem. C 2011, 115 (28), 13739−13750. (13) Nowak, M. J.; Lapinski, L.; Kwiatkowski, J. S.; Leszczyñski, J. Molecular Structure and Infrared Spectra of Adenine. Experimental Matrix Isolation and Density Functional Theory Study of Adenine15N Isotopomers. J. Phys. Chem. 1996, 100 (9), 3527−3534. (14) Xue, Y.; Xie, D. Q.; Yan, G. S. Density functional theory studies on molecular structure and IR spectra of 9-methyladenine: A scaled quantum mechanical force field approach. Int. J. Quantum Chem. 2000, 76 (6), 686−699. (15) Creighton, J. A.; Blatchford, C. G.; Albrecht, M. G. Plasma Resonance Enhancement Of Raman-Scattering by Pyridine Adsorbed on Silver Or Gold Sol Particles Of Size Comparable To the Excitation Wavelength. J. Chem. Soc., Faraday Trans. 2 1979, 75, 790−798. (16) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A., et al. Gaussian 09, D. 01; Gaussian, Inc.: Wallingford CT, 2009. (17) Merrick, J. P.; Moran, D.; Radom, L. An evaluation of harmonic vibrational frequency scale factors. J. Phys. Chem. A 2007, 111 (45), 11683−11700. (18) Krishnakumar, V.; Keresztury, G.; Sundius, T.; Seshadri, S. Density functional theory study of vibrational spectra and assignment of fundamental vibrational modes of 1-methyl-4-piperidone. Spectrochim. Acta, Part A 2007, 68 (3), 845−850. (19) Dennington, R.; Keith, T.; Millam, J. GaussView, Version 5.0.8; Semichem Inc.: Shawnee Mission KS, 2009. (20) Mohamed, T. A.; Shabaan, I. A.; Zoghaib, W. M.; Husband, J.; Farag, R. S.; Alajhaz, A. E. M. A. Tautomerism, normal coordinate

(charge = 2, spin multiplicity =1) are also closer to the measured SERS spectra, maybe due to that adenine still acts as a suitable bidentate ligand on the Ag cluster. For adenine−Au4, the Raman spectra of S11d/S11d1 (charge = 1, spin multiplicity = 2) can also mostly reproduce the measured SERS spectra, while the Raman spectra of S10g/S10g1 (charge = 2, spin multiplicity = 1) are also closer to the measured SERS spectra. In some other structures, adenine do not act as a suitable bidentate ligand on the Ag/Au cluster, such as S10a/S10a1 (charge = 0, spin multiplicity = 1), S10i/S10i1, S11i/S11i1, and the corresponding simulated Raman spectra do not reproduce the measured spectra.

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CONCLUSIONS In summary, the experimental and calculated SERS spectra of 15 N isotope labeled adenine were acquired to clarify the adsorption configuration of adenine on the surfaces of silver and gold nanoparticles. Through comparison of spectral profiles of the experimental and calculated Raman spectra of the isotope labeled adenine with that of the nonisotopic adenine adsorbed on the silver and gold surfaces, we found that the adsorption of adenine on the surfaces silver and gold nanoparticles adopted the same most predominant adsorption configuration in which N7H adenine binds itself with an Au/Ag cluster on both N3 and N9 sites. In addition, we could also make use of the experimental 15N spectra to clarify the weak bands and shoulder bands in the nonisotopic Raman spectra for the identification of the vibrational modes of these bands. As such, we have demonstrated that the combination of simulated and experimental isotopic SERS is a very useful approach to the research of biomolecules adsorption on the metal surface.

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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpcc.7b00818. UV−visible absorption spectra, normal Raman spectra, simulated Raman spectra, and frontier molecular orbitals (PDF)

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AUTHOR INFORMATION

Corresponding Author

*(Q.H.) E-mail: [email protected]. ORCID

Qing Huang: 0000-0002-8884-2063 Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS The authors would like to thank Dr. D. Y. Wu for a helpful discussion and suggestion. This work was supported by USTCSCC Supercomputer Centers, and financially supported by the National Natural Science Foundation of China (No. 11635013 and No. 11475217), the Anhui Provincial Natural Science Foundation (No. 1508085QB44), and the National Basic Research Program of China (No. 2013CB934304).

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REFERENCES

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DFT and SERS Study of 15N Full-Labeled Adenine Adsorption on

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