Nonconventional Hydrogen Bonds between Silver Anion and

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Nonconventional Hydrogen Bonds Between Silver Anion and Nucleobases: Size-Selected Anion Photoelectron Spectroscopy and Density Functional Calculations Peng Wang, Hong-Guang Xu, Guo-Jin Cao, Wen-Jing Zhang, Xi-ling Xu, and Wei-Jun Zheng J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.7b09428 • Publication Date (Web): 31 Oct 2017 Downloaded from http://pubs.acs.org on November 5, 2017

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The Journal of Physical Chemistry

Nonconventional Hydrogen Bonds between Silver Anion and Nucleobases: Size-Selected Anion Photoelectron Spectroscopy and Density Functional Calculations Peng Wang, 1, 3 Hong-Guang Xu, 1, 3 Guo-Jin Cao, *1, 2 Wen-Jing Zhang, 1, 3 Xi-Ling Xu, 1, 3 and Wei-Jun Zheng *1, 3 1

Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular

Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China 2

Institute of Molecular Science, Shanxi University, Taiyuan 030006, China

3

University of Chinese Academy of Sciences, Beijing 100049, P. R. China * E-mail: [email protected], [email protected]

Abstract

We conducted combined gas-phase anion photoelectron spectroscopy and density functional theory studies on nucleobase-silver complexes. The most probable structures of the nucleobase-Ag¯ complexes were determined by comparing the theoretical calculations with the experimental measurements. The vertical detachment energies (VDEs) of uracil-Ag¯, thymine-Ag¯, cytosine-Ag¯ and guanine-Ag¯ were estimated to be 2.18 ± 0.08 eV, 2.11 ± 0.08 eV, 2.04 ± 0.08 eV and 2.20 ± 0.08 eV, respectively, based on their photoelectron spectra. Adenine-Ag¯ has two isomers coexisting in the experiment, the experimental vertical detachment energies (VDEs) of the two isomers are 2.18 and 2.53 eV, respectively. In the most probable isomers of nucleobases-Ag¯, uracil, thymine and cytosine interact with Ag¯ anion via N-H···Ag and C-H···Ag hydrogen bonds, while adenine and guanine interact with Ag¯ anion through two N-H···Ag hydrogen bonds. The N-H···Ag hydrogen bonds can be characterized as medium or strong hydrogen bonds. It is found that binding sites of the Ag anion to the nucleobases are affected by the deprotonation energies (DPEs) and the steric effects of two adjacent X-H groups.

1

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1. INTRODUCTION The interactions between nucleobases and silver nanoclusters have attracted considerable attention in the past decades because of their importance in nanomaterials and biotechnology. DNA chains or oligonucleotides can be used as templates to synthesize ordered and morphology controllable Ag nanoparticles.1-4 It has also been found that DNA-templated silver nanoclusters are efficient fluorescent materials with enhanced chemical stability and low cellular toxicity.5-13 Meanwhile, metal-mediated DNA base pairs resulting from the interactions between DNA bases and silver ion or other metal ions have potential application in DNA-based molecular electronics.14-15 Oligonucleotide-silver nanoparticle conjugates may be used for DNA detection,16-18 diseases diagnosis,19 and drug delivery.20 As silver nanoparticles have increasing applications in diseases diagnosis and drug delivery, it is important to study the interactions between Ag nanoparticles and nucleobases in order to provide insights into the cytotoxicity and genotoxicity of Ag nanomaterials in biological systems.21-23 There are many experimental investigations on the interactions between Ag clusters and nucleobases. The interactions of nucleobases or nucleotides with Ag nanoparticles or Ag thin film were studied using Surface Enhanced Raman Scattering (SERS).24-29 The binding strengths of nucleobases and nucleosides on silver nanoparticles were investigated using colorimetric method.30 The spectrophotometric, potentiometric, and density gradient ultracentrifugation studies revealed that the interactions between silver ion and DNA are influenced by the pH value of the solution, and observed the conversion from N-H···N to N-Ag-N bond between the complementary base pairs.31 The Ag(I)-polyribonucleotides complexes were studied using optical rotatory dispersion and circular dichroism spectroscopy.32 The interaction between Ag ion and free nucleobases in dilute aqueous were investigated by UV and IR dichroic spectroscopy.33 The complexes formed by adenine, guanine and Ag+ were investigated in the gas phase by mass spectrometry and photodissociation experiments.34 In addition, there were numerous theoretical investigations on nucleobase-Ag complexes and nucleobases on silver surface. The excited states of the complexes of adenine tautomers and silver ions were studied using multiconfigurational complete active space (CAS) SCF method and multi-state second order perturbation theory (MS-CASPT2).35The tautomerization, solvent effect and binding interaction of adenine-Ag+ complexes on silver surfaces were investigated by density functional theory.36 The 2


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interactions of adenine with silver surfaces and their effects on the surface-enhanced Raman spectra have also been investigated using density functional method.37 Theoretical studies suggested that the disruptions of the complexes of Ag+ and DNA bases pairs need more energy than the corresponding isolated bases pairs.38 The structures and bonding of Ag(I)–DNA base complexes and Ag(I)–Adenine–Cytosine mispairs were studied by ab initio calculations.39 The properties of small Ag clusters bound to DNA bases were investigated with density functional calculations.40 The theoretical studies on neutral, anionic, and cationic cytosine-Ag and uracil-Ag complexes predicted that in the cationic and neutral complexes, the Ag preferred to bind to the nitrogen or oxygen atoms of nucleobases, whereas in the anionic complexes the Ag atom binds to the nucleobases via the nonconventional hydrogen bonds.41-42 Currently, there is no experimental study on the interactions between silver anion and nucleobases in the literature. To help the understanding of nucleobase-Ag¯ interactions, in this work, we investigate the structures and electronic properties of nucleobase-Ag¯ complexes using size-selected anion photoelectron spectroscopy and density functional theory calculations.

2. EXPERIMENTAL AND THEORETICAL METHODS 2.1 Experimental methods. The experiments were conducted on a home-built apparatus consisting of a laser vaporization cluster source, a time-of-flight mass spectrometer, and a magnetic-bottle photoelectron spectrometer, which has been described elsewhere.43 The Ag-nucleobase complexes were produced by laser-ablation of Ag/nucleobase mixture disk-targets (molar ratios of Ag/nucleobases are 1:5) with the second harmonic (532 nm) of a nanosecond Nd:YAG laser. In order to cool the formed nucleobase-Ag¯ complexes, high purity helium gas with 4-5 atm backing pressure was delivered through a pulsed valve into the source. The Ag-nucleobase complexes were mass-selected and photodetached with the fourth harmonic (266 nm) of another nanosecond Nd:YAG laser. The detached electrons were energy-analyzed by the magnetic-bottle photoelectron spectrometer. The photoelectron spectra were calibrated using the spectra of Cu¯ and I¯ taken under similar conditions. The resolution of the photoelectron spectrometer was about 40 meV for electrons with 1 eV kinetic energy. 2.2 Theoretical methods. We studied the structures of nucleobase-Ag¯ complexes with density functional theory using the B3LYP44-45 functional as implemented in the Gaussian 0946 program package. We used 6-31++G(d, p)47-48 basis set for the C, H, and O atoms and 3



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LanL2DZ49-51 basis set containing an effective core potential for the Ag atoms. The vibrational frequencies were calculated to obtain the zero-point energies and to confirm that the structures are the true local minima. To investigate the influence of different basis sets, the VDEs of nucleobase-Ag anions were calculated using larger basis sets at the B3LYP/aug-cc-pVTZ (for C, N and H atoms) ∪ aug-cc-pVTZ-PP (for Ag atoms) level of theory (Table S1). We noted that the theoretical VDEs of nucleobase-Ag anions did not change much when the different basis sets were used. To confirm the assignments of the isomers contributing to the experimental spectra, the density of states (DOS) simulation was carried out based on theoretically generalized Koopmans’ theorem (GKT).52-53 The peak of each transition in the simulated DOS spectra corresponds to the removal of an electron from a specific molecular orbital of the anion. 54 To perform the energy decomposition analyses on these complexes, the geometries were also optimized with the DFT functional BP8655-56 using the Amsterdam Density Functional program (ADF 2013.01),57-59 converging to an energy gradient < 10-5 Hartree·Å-1 at a Kohn-Sham SCF criterion < 10-8 a.u. The uncontracted Slater basis sets with the quality of triple-zeta plus two polarization functions (TZ2P) were used, with the frozen core approximation applied to the [1s2-3d10] core for Ag, [1s2-4f14] core for Au, the [1s2] cores for C, N and O. The scalar relativistic (SR) was taken into account by the zero order regular approximation (ZORA). The ETS-NOCV energy decomposition approach (EDA) for M¯ + nucleobase → nucleobase-M¯ were analyzed based on the geometric structures of the most probable isomers of nucleobase-M¯ (M = Ag and Au) anions.60-62

UAg-

AAg-

TAg-

GAg-

0.0

0.0

0.5

1.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

Electron Binding Energy (eV)

CAg-

1.5

2.0

2.5

3.0

3.5

4.0

Electron Binding Energy (eV)

Figure 1 Photoelectron spectra of nucleobase-Ag¯ anions recorded with 266 nm photons 4


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Table 1 Relative energies, VDEs and ADEs of the most probable low-lying isomers of nucleobase-Ag anions as well as some key features with the X-H···Ag hydrogen bond obtained by DFT calculations. The bond distances are in angstrom and the bond angles are in degree. BE

Natural

ADE

Isomer ∆E (eV) ∆R (X-H)* R (H···Ag)* ∠X-H···Ag* (eV)

charge

(eV)

Ag UAg¯

¯

TAg

CAg¯

¯

AAg

GAg¯

VDE (eV)

Theo. Expt.

**

1.98

Theo. Expt. **

1A

0.00

0.03

2.59

140.7(N)

0.89

-0.86

2.16

1B

0.42

0.05

2.29

175.0(O)

1.28

-0.74

2.50

2.61

1C

0.55

0.05

2.25

176.8(O)

1.36

-0.73

2.58

2.58

2A

0.00

0.03

2.58

143.4(N)

0.83

-0.86

2.11

2B

0.40

0.04

2.30

174.4(O)

1.22

-0.75

2.47

2.57

2C

0.57

0.03

2.45

157.2(N)

1.51

-0.75

2.73

2.85

3A

0.00

0.02

2.57

172.3(N)

0.73

-0.88

2.05

1.92

1.80

2.24

2.18

2.08

2.18

2.11

2.04

3B

0.040

0.03

2.40

173.7(N)

1.01

-0.81

2.25

2.34

3C

0.065

0.02

2.65

140.4(N)

0.79

-0.87

2.06

2.13

3D

0.096

0.03

2.42

168.5(N)

0.96

-0.83

2.22

2.30

4A

0.00

0.03

2.49

165.3(N)

1.18

-0.81

2.49

2.25

2.60

2.53

4B

0.22

0.03

2.50

153.7(N)

0.62

-0.86

1.93

1.81

2.03

2.18

4C

0.28

0.03

2.47

165.3(N)

1.36

-0.79

2.67

4D

0.42

0.04

2.51

149.2(N)

0.76

-0.84

2.07

5A

0.00

0.02

2.50

164.1(N)

0.82

-0.83

2.16

5B

0.01

0.02

2.50

164.1(N)

0.84

-0.83

2.16

2.76 2.16 1.81

2.26

2.20

2.26

5C

0.23

0.03

2.47

160.6(N)

0.62

-0.85

1.97

2.06

5D

0.26

0.03

2.49

154.0(N)

0.65

-0.86

1.99

2.09

*

For the isomers with two X-H···Ag (X= N, O and C) groups, the parameters of the stronger ones are shown here.

**

The errors of the experimental values are about ±0.08 eV

3. RESULTS 3.1 Experimental results. The photoelectron spectra of nucleobase-Ag¯ anions taken with 266 nm photons are shown in Figure 1. The vertical detachment energies (VDEs) and adiabatic detachment energies (ADEs) of nucleobase-Ag¯ anions estimated from their photoelectron spectra were listed in Table 1. The spectrum of uracil-Ag¯ (UAg¯) has a single feature centered at 2.18 eV, that of thymine-Ag¯ (TAg¯) has a single feature centered at 2.11 eV. The photoelectron spectrum of CAg¯ is dominated by one feature centered at 2.04 eV. There are some noise signals at the high binding energy side in the spectra of UAg¯, TAg¯, and CAg¯, more likely due to the existence of impurities such as the dehydrogenated nucleobase-Ag complexes. The spectrum of guanine-Ag¯ (GAg¯) has a major feature centered at 2.20 eV and an unsolved broad feature above 3.2 eV. The unsolved broad feature above 3.2 eV cannot be 5



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contributed to any most probable isomer, so it more likely comes from the dehydrogenated guanine-Ag¯. The original spectrum of adenine-Ag¯ (AAg¯) has three features centered at 2.18 and 2.53 eV, respectively. Note that the original spectrum of AAg¯ was contaminated by the photoelectron signals from Ag2CN¯, which has mass peaks overlapping with those of AAg¯. The AAg¯ spectrum presented here is obtained by subtract the Ag2CN¯ signals from the original spectrum (details in Figures S1 and S2).

UAg¯

2,4-diketo 1A, 0

2-hydroxy-trans-4-oxo-N3H2-oxo-4-hydroxy-cis-N3H 1B, +0.42 eV 1C, +0.55 eV

2,4-diketo 2A, 0

2-hydroxy-trans-4-oxo-N3H2-hydroxy-cis-4-oxo-N1H 2B, +0.40 eV 2C, +0.57 eV

TAg¯

CAg¯

amino-oxo-N1H 3A, 0

amino-oxo-N3H 3B, +0.040 eV

imino-trans-oxo 3C, +0.065 eV

amino-oxo-N3H 3D, +0.096 eV

amino-N7H 4A, 0

amino-N9H 4B, +0.22 eV

amino-N1H 4C, +0.28 eV

amino-hydroxy-cis 4D, +0.42 eV

K-N7H 5A, 0

K-N9H 5B, +0.01 eV

K-N9H 5C, +0.23 eV

E-N9H-trans 5D, +0.26 eV ¯ ¯

AAg¯

GAg¯

Figure 2 Structures and relative energies of the low-lying isomers of UAg , TAg , CAg¯, AAg¯, and GAg¯ anions. The bond distances are in angstrom (Å) and the bond angles are in degree. 6


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3.2 Theoretical results. In order to obtain the most probable isomers of anionic and neutral nucleobases-Ag, we have considered all possible tautomers of nucleobases reported in the literature63, and optimized their full geometric structures without any symmetry restriction. The typical low-lying isomers of UAg¯, TAg¯, CAg¯, AAg¯ and GAg¯ are shown in Figure 2. UAg¯, TAg¯ and CAg¯ As shown in Figure 2, the low-lying isomers of uracil-Ag¯ anion are planar with CS symmetry. In isomer 1A, the Ag atom interacts with the N1-H and C6-H bonds of the 2, 4-diketo tautomer of uracil. The theoretical VDE of isomer 1A (2.24 eV) is in good agreement with the experimental value (2.18 eV). The ∠N1-H···Ag and ∠C6-H···Ag angles in isomer 1A are 140.7° and 122.6°, respectively. The N1-H and C6-H bonds are elongated by 0.03 Å and 0.01 Å, respectively, relative to those of neutral uracil monomer. In isomer 1B, the Ag atom interacts with the O7-H and N3-H of 2-hydroxy-trans-4-oxo-N3H tautomer of uracil. In isomer

1C,

the

Ag

atom

interacts

with

the

N3-H

and

O8-H

bonds

of

2-oxo-4-hydroxy-trans-N3-H tautomer of uracil. Isomers 1B and 1C are higher than isomer 1A in energy by 0.42 and 0.55 eV respectively. Their theoretical VDE and ADE are much higher than the experimental values. So isomer 1A is the most probable isomer detected in our experiment. The low-lying isomers of TAg¯ are also planar with Cs symmetry. In isomer 2A, the Ag atom interacts with the N1-H and C6-H bonds of the 2, 4-diketo tautomer of thymine. Its theoretical VDE (2.18 eV) is in good agreement with the experimental value (2.11 eV). The ∠N1-H···Ag and ∠C6-H···Ag angles in isomer 2A are 143.4° and 121.0°, respectively. The N1-H bond and C6-H bond are elongated by 0.03 Å and 0.01 Å, respectively, relative to those of neutral thymine monomer. In isomer 2B, the Ag atom interacts with the O7-H and N3-H bonds of 2-hydtoxy-trans-4-oxo-N3H tautomer of thymine. The Ag atom in isomer 2C interacts with the N1-H and O7-H of the 2-hydroxy-cis-4-oxo-N1H tautomer of thymine. Isomers 2B and 2C are higher than isomer 2A in energy by 0.40 and 0.57 eV, respectively. Their theoretical VDEs and ADEs are much higher than the experimental values. So we suggest that isomer 2A is the most probable isomer detected in our experiment. The low-lying isomers of CAg¯ are quasi-planar with C1 symmetry. The Ag atom in the lowest-lying isomer (3A) interacts with the N8-H and the C5-H bonds of the amino-oxo-N1H tautomer of cytosine. Its theoretical VDE (2.08 eV) is in good agreement with the 7



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experimental value (2.04 eV). The ∠N8-H···Ag and ∠C5-H···Ag angles in isomer 3A are 172.3° and 139.3°, respectively. The N8-H bond and C6-H bond are elongated by 0.02 Å and 0.01 Å compared with those of neutral cytosine. Isomers 3B, 3C and 3D can be considered as the Ag atom interacting with the amino-oxo-N3H, imino-trans-oxo, and amino-oxo-N3H tautomers of cytosine, respectively. They are higher in energy than isomer 3A by only 0.04, 0.065 and 0.096 eV, respectively. The theoretical VDEs of isomers 3B, 3C and 3D are also consistent with the experimental value. Thus, isomer 3A is the most probable one contributing to the experimental spectrum of CAg¯, isomers 3B, 3C and 3D may also contribute to the experimental spectrum. AAg¯ and GAg¯ The low-lying isomers of AAg¯ have quasi-planar structures with C1 symmetry. In the lowest-energy isomer (4A), the Ag atom interacts with the amino hydrogen and N7-H of amino-N7H tautomer of adenine, the theoretical VDE of isomer 4A (2.60 eV) is in good agreement with the second peak in the experimental photoelectron spectrum of AAg¯ (2.53 eV). The ∠N7-H···Ag and ∠N10-H···Ag angles in isomer 4A are 165.3° and 169.2°, respectively. The N7-H bond and N10-H bond are elongated by 0.03 Å and 0.01 Å in isomer 4A relative to those of neutral adenine monomer. Isomer 4B is higher in energy than isomer 4A by 0.22 eV. The theoretical VDE of isomer 4B (2.03 eV) is in good agreement with the first peak in the experimental photoelectron spectrum of AAg¯ (2.18 eV). Therefore, it is possible that isomers 4A and 4B coexist in the experiment. Isomers 4C and 4D are higher than 4A by 0.28 eV and 0.42 eV, respectively. In isomers 4B, 4C and 4D, the Ag atoms interact with the amino-N9H, anino-N1H and amino-hydroxy-cis tautomers of adenine. Isomer 4D is much less stable than isomer 4A, although its theoretical VDE and ADE (2.16 eV and 2.07 eV) are in agreement with the first peak in the experimental photoelectron spectrum. The low-lying isomers of GAg¯ have quasi-planar structures with C1 symmetry. Isomers 5A and 5B are almost degenerate in energy. In isomer 5A, the Ag atom interacts with the N1-H and N10-H bonds of the K-N7H tautomer of guanine. The theoretical VDE of 5A (2.26 eV) is in excellent agreement with the experimental value (2.20 eV). The ∠N1-H···Ag and ∠N10-H···Ag angles are 148.7° and 164.1°. The N1-H and N10-H bonds are elongated by 0.02 Å in isomer 5A relative to those of neutral guanine monomer. The Ag atom in isomer 5B interacts with the N1-H and N10-H bonds of the K-N9H tautomer of guanine. The theoretical VDE of isomer 5B is also in agreement with the experimental value. More likely, isomers 5A 8


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and 5B coexist in the experiment. Isomers 5C and 5D are higher in energy than isomer 5A by 0.23 and 0.26 eV, respectively. Their theoretical VDEs are slightly lower than the experimental value.

4. DISCUSSION The natural bond orbital (NBO)64 analysis was conducted to understand the electronic structures and bonding properties of nucleobase-Ag¯ complexes. As the NBO analysis of charge distributions shown in Table 1, the extra electron of each nucleobase-Ag¯ anion mainly localizes on the Ag atom, thus, the Ag atom is negatively charged. We also plotted the highest occupied molecular orbitals (HOMOs) of the most stable isomers of nucleobase-Ag¯ complexes in Figure 3. It can be seen from Figure 3 that the HOMOs of these complexes mainly consist of Ag 5s orbital, hence, the electron clouds of the HOMOs mainly localize on the Ag atom. The localization of the HOMOs on Ag is in good agreement with the results of NPA charge distributions.

UAg¯

TAg¯

AAg¯

CAg¯

GAg¯

Figure 3 Highest occupied molecular orbitals (HOMOs) of the most stable isomers of nucleobase-Ag¯ complexes. In the most probable structures of UAg¯, TAg¯ or CAg¯, the Ag anion interacts with the 9



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N-H and C-H bonds of U, T or C, therefore, there are N-H···Ag and C-H···Ag units in the most probable structures of UAg¯, TAg¯ and CAg¯. In the most probable structure of AAg¯ or GAg¯, the Ag anion interacts with two N-H bonds of A or G, hence, there are two N-H···Ag units in the most probable structures of AAg¯ and GAg¯. The H···Ag distances of these complexes range from 2.25 Å to 2.87 Å, smaller than the sum of the van der Waals radius of H (1.20 Å)65 and Ag (1.72 Å).66 The N-H or C-H bonds interacting with Ag anion are lengthened by 0.01-0.05 Å compared with those in free nucleobases. The X-H···Ag units in these complexes are close to linear arrangement. It is worth mentioning that the X-H···Ag units are different from the agostic bonds (C-H···M), in which the M is also a transition metal atom.67 The typical agostic bond involves three centers two electrons (3c-2e) interaction,68-69 while the X-H···Ag bonds have three centers four electrons (3c-4e) character. Moreover, the transition metal atom M in agostic bond is usually more electropositive, and the electrons are transferred from C-H σ orbital to transition metal M; whereas in the nucleobase-Ag¯ anions, the extra electron mainly localizes on the Ag atom with a part of the negative charge transfer from Ag¯ anion to the X-H σ* bonds. All the structure details the X-H···Ag units are consistent with the definition of hydrogen bonds proposed by International Union of Pure and Applied Chemistry (IUPAC).70 Therefore, the X-H···Ag units in nucleobases-Ag¯ anions can be considered as nonconventional hydrogen bonds. By looking at the most probable structures of CAg¯, AAg¯ and GAg¯ which contain amino groups, one can find that the Ag anion prefer interacting with a N-H bond of amino group although it has a low deprotonation energy (DPE), which should be due to the steric effects that the amino group and the adjacent X-H can provide more suitable orientation to construct two stronger quasi-linear X-H···Ag bonds, in other words, the influence of steric effects to the interaction between nucleobases and Ag anion is larger than that of DPEs.

Here, we compare the N-H···Ag bond with N-H···O conventional hydrogen bond. The typical bond angles of N-H···O bonds are in range of 127°-177°, while those of the N-H···Ag bonds in nucleobases-Ag complexes anions vary between 131.2° and 178.5°. As shown in Table 1, the nucleobase-Ag¯ binding energies are in the range of 0.62-1.36 eV. For nucleobase-Ag¯ anions consisting of a strong N-H···Ag bond and a weaker X-H···Ag (X = N or C), the strength of N-H···Ag bonds should be larger than half of the nucleobase-Ag¯ binding energies. According to the criterion of hydrogen bonds,71 the N-H···Ag bonds in nucleobase-Ag¯ anions can be considered as medium (0.17-0.65 eV) or strong (higher than 10


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0.65 eV) hydrogen bonds.

Table 2 Properties of the electron density at the bond critical points for the N-H···Ag and C-H···Ag bonds in nucleobases-Ag cluster anions. Bond critical point UAg¯ CAg¯ TAg¯ AAg¯ GAg¯

N-H···Ag C-H···Ag N-H···Ag C-H···Ag N-H···Ag C-H···Ag N-H···Ag N-H···Ag N-H···Ag N-H···Ag

ρ(r) (|e|•Bohr-3) 0.0151 0.0087 0.0150 0.0058 0.0154 0.0079 0.0179 0.0119 0.0174 0.0107

∇2ρ(r) (|e|•Bohr-5) 0.0251 0.0170 0.0246 0.0108 0.0253 0.0154 0.0275 0.0195 0.0288 0.0177

λ1 (|e|•Bohr-5) 0.0476 -0.0043 0.0478 0.0166 0.0487 0.0235 0.0563 0.0362 0.0562 0.0315

λ2 (|e|•Bohr-5) -0.0112 0.0266 -0.0116 -0.0025 -0.0116 -0.0035 -0.0143 -0.0082 -0.0136 -0.0066

λ3 (|e|•Bohr-5) -0.0114 -0.0053 -0.0116 -0.0033 -0.0118 -0.0046 -0.0145 -0.0085 -0.0139 -0.0072

ε 0.0215 0.2305 0.0041 0.2960 0.0152 0.3291 0.0148 0.0319 0.0232 0.0940

To further study the nature of the nonconventional hydrogen bonds in these nucleobase-Ag complexes, we performed the topological analysis by the means of atom in molecular (AIM)72 to calculate the electron density, the Laplacian of the electron density at the bond critical points (BCPs) using the Multiwfn software.73 The electron densities (ρ(r)), Laplacian of electron densities (∇2ρ(r)), Hessian eigenvalues of the electron densities (λ1, λ2 and λ3) and ellipticities (ε = λ1/λ2-1) at the bond critical points (BCPs) for the nucleobases-Ag¯ anions are shown in Table 2. The topological analysis indicates that the BCPs of (3, -1) topology and bond paths linking the H atom and Ag atom exist in all X-H···Ag bonds, and all the BCPs are not near the ring critical points (RCPs). The values of electron density (ρ(r)) in all BCPs are above zero and in the proposed range of 0.002-0.035 suggested by Popelier.74-75 The Laplacian of electron density (∇2ρ(r)) in all BCPs of the most significant X-H···Ag bonds are also positive and in the range of 0.024-0.139.74-75 Thus, we can affirm the existence of nonconventional hydrogen bonds X-H···Ag between Ag¯ and nucleobases. Furthermore, the values of electron density (ρ(r)) and Laplacian of electron density (∇ 2ρ(r)) are closely correlated with the bond strengths and bond types.76 According to the values of electron density (ρ(r)), the (strongest) N-H···Ag bonds of AAg¯ and GAg¯ (with purine rings) are stronger than those of UAg¯, TAg¯ and CAg¯ (with pyrimidine rings), which should be 11



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attributed to the larger conjugate symmetry of purine rings. Table 3 Energy decomposition analysis for M¯ + nucleobase → nucleobase-M¯ (M =Au and Ag) from BP86/TZ2P calculations. The energies are in eV. M

∆Eelstat

∆EPauli

∆ESter

∆EOrb

∆Eint

UAg¯ UAu¯ TAg¯ TAu¯ CAg¯ CAu¯ AAg¯ AAu¯ GAg¯ GAu¯

-1.22 -1.34 -1.14 -1.28 -1.01 -1.14 -0.95 -1.11 -1.22 -1.42

0.82 0.91 0.77 0.88 0.67 0.76 0.70 0.86 0.88 1.07

-0.40 -0.43 -0.37 -0.40 -0.34 -0.38 -0.25 -0.25 -0.34 -0.35

-0.59 -0.78 -0.55 -0.75 -0.50 -0.66 -0.54 -0.77 -0.70 -0.93

-0.99 -1.21 -0.92 -1.15 -0.84 -1.04 -0.79 -1.02 -1.04 -1.28

It is interesting to compare the N-H···Ag hydrogen bonds with the N-H···Au hydrogen bonds which were studied previously.77-78 The bond angles of N-H···Au bonds are in the range of 133.7°-179.5°, while those of N-H···Ag bonds vary between 131.2°-178.5°. The elongations of N-H in nucleobases-Ag¯ complexes (0.02-0.04 Å) are less significant than those of nucleobases-Au¯ complexes (0.03-0.05 Å). Furthermore, we compared the binding energies of nucleobases-Au¯ complexes and nucleobases-Ag¯ complexes. It is found that the binding energies of nucleobases-Au¯ complexes (0.63-1.54 eV) are higher than those of nucleobases-Ag¯ complexes (0.62-1.51 eV). We performed ETS-NOCV EDA analysis to obtain a deeper insight into the nucleobases-Au/Ag¯ qualitatively. Table 3 shows the details of the total interaction energies ∆Eint of M¯ anion (M = Au and Ag) with nucleobases, M¯ + nucleobase → nucleobase-M¯, the interaction energies can be divided into ∆Eelstat, ∆EPauli, and ∆Eorb by ∆Eint = ∆Eelstat + ∆EPauli + ∆Eorb.79 Here, ∆Eelstat is the quasi-classical Coulomb interaction energy in the overlapping between the valence electron shells of the nucleobase and M¯ anion. The repulsive exchange interactions between electrons of the two fragments (M¯ ion and nucleobase) are termed as ∆EPauli. ∆Eorb is the covalent contribution to the chemical bond in nucleobase-M¯ cluster anions. The sum of ∆Eelstat and ∆EPauli is equal to the steric interaction energy (∆ESter). All the energy terms including ∆Eelstat, ∆EPauli, ∆Eorb and ∆Eint for nucleobase-Au¯ anions have larger absolute values than those of nucleobase-Ag¯ 12


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anions, in agreement with the order of their binding energies. As defined by IUPAC, the hydrogen bonds are attractive interaction between a hydrogen atom and another atom (X) or a group of atoms.70 More charge localizes on Au anions results stronger electrostatic interactions (∆Eelstat) between Au¯ and nucleobases than those between Ag¯ and nucleobases, however, the repulsive exchange interactions (∆EPauli) of nucleobase-Au¯ are also larger than those of nucleobase-Ag¯. In other words, the steric interactions consisted by ∆Eelstat and ∆EPauli of nucleobase-Au¯ are close to those of nucleobase-Ag¯, the differences of the total interaction energies between nucleobase-Au¯ and nucleobase-Ag¯ are mainly from the differences of the covalent contribution (∆Eorb), which comes from the orbital mixing.62

5. CONCLUSIONS We measured the photoelectron spectra of nucleobase-Ag¯ complexes and investigated their structures with density functional calculations. Compared the experimental and theoretical results, we determined the structures of nucleobase-silver complexes. The existence of nonconventional hydrogen bonds between nucleobases and Ag¯ anion is confirmed. For nucleobases without amino group, the Ag¯ anion prefers to bind to the N-H bonds with lower DPEs; for the nucleobases with amino group, the Ag¯ anion prefers to interact with the amino group and the adjacent X-H bond. The stability of nucleobase-Ag¯ depends on not only the binding energies of nucleobases-Ag¯ interactions, but also the influence of the proton transfer energies.

ASSOCIATED CONTENT Supporting Information The details for removing the contaminations in the spectrum of AAg¯; more complete list of low-lying isomers; the comparison of experimental spectra with simulated DOS spectra; the comparison of the results at small basis set and large basis set. This material is available free of charge via the Internet at http://pubs.acs.org.

AUTHOR INFORMATION Corresponding Author *Corresponding authors. E-mail: [email protected] (G.-J.C.), [email protected] (W.-J. Z.) 13



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Notes The authors declare no competing financial interests.

ACKNOWLEDGEMENTS This work was supported by the Natural Science Foundation of China (Grant No. 21273246 and 21501114), the Natural Science Foundation of Shanxi Province (Grant No. 2015021048), and the Open Fund of Beijing National Laboratory for Molecular Sciences (Grant No. BNLMS20150051). The theoretical calculations were conducted on the ScGrid of the Supercomputing Center, Computer Network Information Center of the Chinese Academy of Sciences.

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Nonconventional Hydrogen Bonds between Silver Anion and

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