Computational Study on the Interaction of Modified Nucleobases with

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Computational Study on the Interaction of Modified Nucleobases with Graphene and Doped Graphenes Sathish Kumar Mudedla, Kanagasabai Balamurugan, and Venkatesan Subramanian J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/jp503126q • Publication Date (Web): 30 Jun 2014 Downloaded from http://pubs.acs.org on July 8, 2014

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The Journal of Physical Chemistry

Computational Study on the Interaction of Modified Nucleobases with Graphene and Doped Graphenes S. K. Mudedla a,b, K. Balamurugan a and V. Subramanian a,b,* a

Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai-600 020, India b

Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg,

New Delhi 110 001, India

Abstract The interaction between graphene based nanomaterials and modified nucleobases (MBs) is important in the development and designing of new biosensors. The adsorption of MBs on the surface of graphene (G), boron doped graphene (BG), nitrogen doped graphene (NG) and silicon doped graphene (SiG) have been investigated using electronic structure calculations and associated analysis methods. It is found from the calculations that the MBs stack with the surface of G, BG, NG and SiG models and the π-π stacking interaction plays a predominant role in the stabilization of the inter-molecular complexes. The stability of MBs on the surface of SiG is the highest when compared to G, BG and NG models. The highest interaction energies of MBs with SiG is due to the presence of Si….O(N) and π-π stacking interactions. The theory of Atoms in Molecules (AIM) analysis indicates that Si….O(N) interaction has both electrostatic and covalent characters. The calculation of charge transfer by employing NBO method showed that the donor nature of MBs. It is also found that the variations in the density of states and HOMOLUMO gap of SiG occur upon adsorption of MBs. These results illustrate that SiG can act as a sensor for the detection of MBs. Keywords: Graphene, doped graphene, modified bases, dispersion interaction, charge transfer and density of states. * To whom correspondence should be addressed. Tel.: +91 44 24411630. Fax: +91 44 24911589. E–mail: [email protected], [email protected].

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Introduction Graphene has fascinated many researchers due to its extraordinary properties and concomitant applications in different fields.1-5 Hence, the possible applications of graphene and its derivatives in different fields such as nanoelectronics, engineering nanocomposite materials, energy storage,

field effect transistor, sensors, catalysis, biology and medicine have been

envisaged and investigated.6-14 From the stand point view of applications in biology and medicine, the interaction of bio-molecules with graphene and its derivatives has also received considerable interest. The large surface area of graphene facilitates the adsorption of biomolecules and gas molecules.15-21 Functionalized graphene was used to distinguish the different nucleobases in the sequencing of DNA.22 It is found that graphene can be used for the removal of pesticides and pollutants.23,24 The detection of adsorbed molecules on the graphene is possible due to its high conductivity and concomitant charge transfer between the interacting partners.25 The adsorption strength of molecules on graphene can be modulated by doping graphene with elements such as boron, nitrogen, silicon, aluminum, phosphorus and sulphur and also by topological defects.26-31 The usefulness of pristine and modified graphene in the field of catalysis has been widely explored.32,33 Functionalization of graphene by epoxide and nitrogen has been shown to reduce dioxygen at ambient conditions through experimental and theoretical studies.34 Similarly, recent computational investigation have established that both boron doped and hydrogen decorated graphene sheets act as better catalysts for oxygen reduction when compared to pristine graphene.35 Previous reports reveal that silicon doped graphene is useful in the sensing of gases and it acts as a metal free catalyst in the reduction of N2O.36,37 Silicon doped graphene can be used as a sensor for both NO and NO2.38 In addition to the doped graphene, several theoretical studies have revealed that the doped carbon nanotube can be used for the


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detection of biomolecules and organic pollutants.

39,40

The introduction of boron dopant in

carbon nanotube increases the adsorption strength of amino acid on its surface.41 Although, the local topological structure of both graphene and carbon nanotube doped with boron, nitrogen and silicon is similar, the electronic structure is different from each other.42-46 Silicon doping causes the localized structural changes in both silicon doped carbon nanotube and silicon doped graphene. The doping of silicon in semiconducting carbon nanotube closes its band gap by the introduction of new band nearer to the conduction band.44 The metallic nature of carbon nanotube is changed to semiconductor with the doping of silicon.44 In the case of graphene, the zero band gap was opened up with the introduction of silicon.46 It is also well known that the planarity of doped graphene is high in contrast to carbon nanotube and concomitantly surface area available for the adsorbent increases appreciably. Many studies have elicited that the curvature is inversely related to the strength of the interaction between carbon nanomaterials and biomolecules.16,47 Therefore, the interaction between biomolecules with graphene and doped graphenes (boron, nitrogen and silicon doped graphene) would be high compared to doped carbon nanotube. Therefore, these doped graphenes have selected in the present study. These systems may efficiently interact with the molecules and they may also provide very good molecular systems for the development of sensors. Purine bases (adenine, guanine) are building blocks of the three dimensional structure of DNA and RNA. In purine metabolism of human beings, the compounds such as uric acid, xanthine and hypoxanthine are evolved as oxidation products.48 Caffeine is a methyl derivative of xanthine and it is introduced into the body fluids by drinking tea, coffee and coca cola.49 The concentration levels of these modified nucleobases (MBs) (uric acid, xanthine, hypoxanthine and caffeine) in blood and urine are sensitive indicators for several pathological states including gout,



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hyperuricaemia, pneumonia, xanthinuria, stimulation of central nervous system and positive effect on cardiovascular system.50-54 Therefore, the accurate detection and quantification of MBs in body fluids are important for clinical diagnosis.55 Various techniques have been developed to determine the MBs, including, high pressure liquid chromatography, capillary electrophoresis enzymatic methods and electrochemistry methods.56-63 However, the requirement of expensive apparatus, fastidious sample preparation and expensive material, hampers further applications of these methods. In this context, simple electrochemical methods may be a good alternative strategy when compared to above-mentioned methods. The chemically modified electrodes have become important for the electrochemical detection of biologically important compounds.64 It is evident from earlier investigations that carbonaceous nano materials have been used for the development of electrodes for various applications.65,66 The electrodes developed from the carbon nanotube and multi-walled carbon nanotubes were exploited as electrodes for the detection of MBs.67,68 Graphene was used as a platform for the detection of caffeine in food beverages.69,70 Alwarappan and co-workers have found that graphene electrodes act as a better biosensor than carbon nanotubes.71 The same authors showed that the strength of adsorption of molecules on graphene is important for their electrochemical detection.72 Graphene oxide and reduced graphene oxide are used for the real-time detection of MBs.73 Reduced graphene oxide showed improved electrocatalytic activity due to its π-π interaction with MBs.73 Therefore, molecular level understanding of the interaction between MBs and graphene based materials has become imperative for the development of new sensors. In this study, an attempt has been made to explore the interaction of MBs with graphene, B-, N- and Si-doped graphenes using electronic structure methods. The following points have been addressed in this study:


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1. To determine the strength of the interaction of MBs with graphene and also with its doped models (B-doped graphene, N-doped graphene and Si-doped graphene). 2. To compare the strength of adsorption of MBs on graphene and also on doped graphenes 3. To assess the nature of interaction between the two systems. 4. To understand the changes in the electronic structure of graphene models upon adsorption of MBs.

Computational Methodology The structure of graphene model was taken from previous study.74 The graphene model contains 42 carbon atoms and the edge carbon atoms were passivated with hydrogens. The molecular formula of graphene model is C42H16. The density functional theory (DFT) based methods such as M06-2X, ωB97XD and B3LYP-D are widely used to study the structure and energetics of weakly bonded systems.16,75 Hence, these functional were selected in this study. The geometry of graphene model was optimized at M06-2X/6-31+G** level of theory. In this investigation, pristine graphene was doped with boron (B), nitrogen (N) and silicon (Si) atoms. The position of doped atom was chosen based on the previous studies.76 All doped models were optimized at the same level of theory. The MBs were also optimized with M06-2X/6-31+G** method. Caffeine, hypoxanthine, uric acid and xanthine are represented as CAF, HX, UA and X in the remaining part of the text. Graphene models are represented as pristine graphene (G), boron doped graphene (BG), nitrogen doped graphene (NG) and silicon doped graphene (SiG). The optimized geometries are shown in Figure 1. Both BG and NG exhibit planar geometry akin to that of pristine graphene. In SiG, silicon is projected out of the basal plane of graphene due to longer Si-C (1.75 Å) bond in contrast to C-C (1.34 Å) bond. The calculated bond length of B-C,



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N-C and Si-C is 1.49, 1.40 and 1.75 Å, respectively and these values are in close agreement with previous reports.76,77 The inter-molecular complexes of MBs with graphene models (G, BG, NG and SiG) were optimized at M06-2X/6-31+G** level of theory. The interaction energies were calculated with the help of supramolecular approach using the following equation employing M06-2X/6-311+G**, B3LYP-D/6-311+G** and ωB97XD/6-311+G** method, for the geometries as obtained from the M06-2X/6-31+G** calculations. Interaction Energy = (EAB- (EA+EB))

(1)

Where EAB is the energy of the complex formed between graphene model and MBs. Both EA and EB denote the energies of graphene model and MBs, respectively. The interaction energies were corrected for the basis set superposition error (BSSE) using the counterpoise method suggested by Boys and Bernadi.78 The Natural Bond Orbital (NBO) analysis was carried out to quantify the charge transfer between graphene models and MBs at M06-2X/cc-pVDZ level. All the calculations were carried out using Gaussian 09 suite of programs.79 The electron density difference was calculated by using the program MultiWave.80 The theory of Atoms in Molecules (AIM) was used to characterize the both covalent and non-covalent interactions.81-83 In this study, AIM was employed to understand the nature of the interaction between graphene models and MBs. The wave function generated from M06-2X functional with 6-31+G** basis set, was used for AIM calculation employing AIM2000 package.84 The energy decomposition analysis (EDA) was performed using dispersion corrected Grimme’s functional, BLYP-D, available in Amsterdam Density Functional Theory (ADF) package.85-87 The sensitivity of graphene models towards adsorption of MBs was further analyzed by the calculation of density of states (DOS) using GaussSum program.88


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Results and Discussion The calculated molecular electrostatic potential isosurface (ESP) for MBs are given in Figure 2, in which red and blue colors represent positive and negative potential regions. The active centers such as CO and N, in MBs are highlighted in Figure 2. These active centers correspond to negative electrostatic potential isosurfaces in Figure 2. These active centers were made to interact with the pristine and doped graphenes in two different modes: (i) the active centers were kept perpendicular to basal plane of the graphene and (ii) MBs were also placed parallel to the basal plane of the graphene. These initial geometries were considered for energy minimization. The optimized geometries as obtained from M06-2X/6-31+G** level of calculation are shown in Figure 3. The calculated vertical rise between the graphene models and MBs varies from 3.1-3.4 Å. Close scrutiny of the geometries shows that MBs stack with the G, BG, NG and SiG through π-π interaction. The closest distance between the active center and the carbon atom in the G, BG, and NG ranges from 3.1 to 3.5 Å. The same between MBs with SiG varies from 1.8-1.9 Å. It is interesting to note from the results that the molecule HX interacts only through the perpendicular mode with the surface of SiG. The π-π stacking is not found in this inter-molecular complex. The calculated interaction energies at M06-2X/6-311+G** using counterpoise method are shown in Table 1. It can be seen from Table 1, the BSSE uncorrected values are higher than the corrected values. These results show that the importance of BSSE in these complexes. In addition to M06-2X/6-311+G**, the interaction energies were calculated at B3LYP-D/6-311+G** and ωB97XD/6-311+G** levels and are presented in Table 1. The trend in the interaction energies is same for all the functionals. It can be noted that the trend in the interaction energies of MBs with G and BG is similar. It varies as CAF > UA > X > HX. In the case of NG, the trend in the interaction energy is CAF > UA > HX > X and it is not same as G



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and BG. From the geometrical features (stacking pattern) of optimized structures, it can be clearly noted that the dispersion interaction plays a dominant role in the stabilization of the intermolecular complexes. Hence, the polarizability of the MBs was calculated to understand the trend in the interaction energy. The calculated polarizability for CAF, UA, X and HX is 122.65, 92.67, 86.63 and 83.22 Bohr3, respectively. The strong interaction between CAF and models of graphene can be attributed to its highest polarizability.89 In the case of SiG model, significant increase in the interaction energy has been found. The order of interaction energies is found to be X > CAF > UA > HX. This trend is different from the interaction of MBs with other graphene models. The trend in the interaction energy does not in parallel with the polarizability whereas the dipole moment of MBs exhibits linear relationship with the calculated interaction energy. The calculated dipole moment of X, HX, CAF and UA is 7.4, 5.1, 4.0, and 3.1 Debye which indicates the role of electrostatic interaction in the stabilization of inter-molecular complexes. The interaction energy of HX is lower than that of UA and CAF due to the absence of π-π stacking. It can be seen from the geometrical features of the SiG-MB complexes, both Si….O (N) and π-π stacking interactions are responsible for their highest interaction energies. To understand further, the electron density isosurfaces of the frontier orbitals were calculated and the results are shown in Figure 4. It can be seen that both highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of SiG have significant contribution from Si atom. The silicon in SiG can act as a reactive site for both electrophilic and nucleophilic attacks. In this context, it is interesting to note from the previous work of Zhao et.al that the electrophilic nature of Si is slightly higher than that of nucleophilic character.77 The electrophilic nature is the reason for the strong interaction between Si and O (N). The EDA is used to understand the nature of interaction between SiG and MBs.


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EDA decomposes the interaction energy between two monomers into several meaningful components, including electrostatic energy, orbital energy, Pauli repulsion and dispersion energy. The results obtained from the EDA are presented in Table 2. It can be noted from the results that the electrostatic energy is the predominant interaction in the stabilization of the intermolecular complex. In addition to the electrostatic interaction, orbital interaction plays a crucial role in the stabilization of these complexes. The contribution from dispersion energy is marginal when compared to electrostatic and orbital interactions. The theory of AIM is used to understand the interaction between the partners in the formation of inter-molecular complexes.81-83 The analysis of electron density ρ(rc) at the bond critical points (BCPs) is used to describe the strength of the bond.90 The Laplacian of the electron density (∇2ρ (RC)) provides further valuable information about the bonding. A negative value of ∇2ρ(rc) indicates the concentration of the electron density along the bond and is usually related to covalent bonds. A positive value of ∇2ρ(rc) shows that a local depletion of the electron density occurs at the BCP, suggesting a closed shell (electrostatic, hydrogen bond and π-π stacking) interaction. The molecular graphs for the various complexes as obtained from the AIM analysis are depicted in Figure 5. It can be seen that bond critical points are found between the two stacked units. The calculated topological parameters are listed in Table 3. The sum of electron density is high for the SiG-MB complexes when compared to other models. The signature of ∇2ρ(rc) at each BCP in all the complexes is found to be positive and it represents the noncovalent nature of interaction. The electron density ρ(rc) at the BCP is of the order of (0.1 a.u) for covalent bonds while in the case of non-covalent interactions, it is one order lower (0.01 a.u or even less). The ρ(rc) values (0.07- 0.08 a.u) at BCPs between Si and O(N) in SiG-MBs complexes lie in between the values corresponding to the non-covalent and covalent interactions.



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The ∇2ρ(rc) is related to other properties such as potential energy density (Vc), kinetic energy density (Gc) and total energy density (Hc). The relation between these parameters and ∇2ρ(rc) is given below 1/4∇2ρ(rc) = 2Gc+ Vc

(2)

Hc = Gc + Vc

(3)

It is found from previous reports that the inter-molecular interactions have been characterized using the Hc values.91,92 Thus, to gain further insight into the nature of interaction, the total energy density (Hc) value at BCP between Si and O(N) was obtained from the equation 3. The calculated values are listed in Table 4. If the value of Hc is positive, then the interaction is non-covalent in nature and otherwise, it is covalent in nature. From Table 4, it can be found that the signature of ∇2ρ(rc) is positive and the values of Hc are negative for all complexes of Si doped graphene. Therefore, the interaction Si…O (N) is partially electrostatic and partially covalent in nature. The formation of inter-molecular complex between SiG and MBs is governed by both Si….O(N) and π-π stacking interactions. These findings are in close agreement with the information obtained from the EDA analysis. The calculated NBO charges of MBs are presented in Table 5. Results show that the charge transfer between G, BG and NG models and MBs is negligible. Whereas, considerable charge transfer between SiG and MBs can also be noted from the results. The positive sign of values indicates that the charge is transferred from MBs to SiG. The calculated orbital interaction energies from second order perturbation theory approach of Fock matrix using the NBO analysis are in Table 6. The maximum E(2) values are found for the interaction between lone pair of O (N) and unoccupied orbital of Si. This finding clearly reveals that the charge transfer interaction


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plays an important role in the formation of the inter-molecular complex between SiG and MBs. The isosurface of electron density difference was calculated by subtracting the electron density of monomers from that of inter-molecular complex. The calculated electron density difference for the complex of MBs and SiG is given in Figure 6 (blue color represent increased electron density and red color indicates decreased electron density). From Figure 6, it can be seen that the charge transfer takes place from oxygen to silicon. Further, there are no changes in electron density between the π systems of SiG and MBs. The charge transfer may change the SiG electronic structure implying variations in its conductivity. To understand the changes in electronic structure of graphene models, DOS for various systems was calculated. The results are presented in Supporting Information (Figures S1-S4). Both DOS and HOMO-LUMO gap of G, BG and NG do not change upon adsorption of MBs. However, the DOS features change upon adsorption of MBs on the surface of SiG. The HOMO-LUMO gap of SiG is 3.70 eV. On the other hand, the HOMO-LUMO gap of SiG undergoes change after the adsorption of MBs. The HOMO-LUMO gap values are presented in Table 7. The reduction in the energy gap is ~ 0.1, 0.3, 0.4 and 0.4 eV by CAF, HX, UA and X, respectively. The partial density of states (PDOS) for the SiG-MBs complexes is depicted in Figure 7. As it can be seen from Figure 7 that the LUMO level arises from the contribution of MB orbitals in all the complexes except Si-CAF. Both HOMO and LUMO of SiG-MB complexes are shown in Figure 8. The HOMO of the complexes is localized over the SiG and LUMO is distributed over the MBs. In the case of SiCAF, both HOMO and LUMO are localized on SiG. These observations are in agreement with the PDOS of these complexes. The localized changes in the DOS particularly at LUMO are expected to bring variations in the corresponding conductivity of the complex.36 These results (changes in HOMO-LUMO gap and DOS) confirm that there is a variation in the electronic



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structure of the SiG-MB complexes which leads to changes in the conductivity of the SiG model. Although, the doping concentration is low, it is expected to bring changes in the electronic structure and associated conductivity of doped graphene. These changes in the conductivity can be beneficially exploited to design new sensors. Similar findings have also been reported in the previous studies.36,40 Conclusion The adsorption of MBs on the surface of G, BG, NG and SiG has been studied using electronic calculations and associated analysis tools. The strength of adsorption of MBs on the surface of SiG is the highest when compared to that with the surface of G, BG and NG models. Scrunity of results from the AIM analysis shows that the π-π stacking interaction is the main determining factor for the adsorption of MBs on the various surfaces. Furthermore, the maximum adsorption strength of MBs on the surface of SiG is due to the presence of Si….O(N) interaction between SiG and MBs. Interesting to note from the systematic AIM analysis that the Si….O (N) interaction has both electrostatic and covalent characters. The NBO analysis points out that there is a negligible charge transfer between G, BG and NG and MBs. On the other hand, the charge transfer is the maximum between SiG and MBs. The strong adsorption of MBs on the surface of SiG leads to changes in the HOMO-LUMO gap of the inter-molecular complex and the DOS at the frontier levels. These variations in the electronic structure and associated changes in the electronic properties are useful for the designing of new sensors employing silicon doped graphene. Overall, findings from this study affirm that SiG can act as a sensor for the detection of MBs. Experimental investigations have pointed that the silicon doped carbon quantum dots can be used to sense the molecules such as H2O2 and melamine.93 Therefore, current findings may kindle further experimental studies in this direction.


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Supporting Information Density of states (DOS) for Graphene (G), B-doped graphene (BG), N-doped graphene (NG), Sidoped graphene (SiG) and the complexes of G, BG, NG and SiG with MBs. This material is available free of charge via the Internet at http://pubs.acs.org. Acknowledgements We thank the Board of Research in Nuclear sciences (BRNS), Mumbai, India, and Nanomaterial – Safety, Health and Environment (NanoSHE BSC0112) project funded by Council of Scientific and Industrial Research (CSIR) New Delhi, India, for Financial Support. M. S. K thanks Department of Sceince and Technology (DST), New Delhi, India for providing INSPIRE Fellowship (Inspire Fellow). K. B thanks Council of Scientific and Industrial Research (CSIR) New Delhi, India, for providing Senior Research Fellowship (SRF).



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TABLE 1. The Calculated Interaction Energies of MBs with Graphene Models (G, BG, NG and SiG) at M06-2X/6-311+G**, B3LYP/6-311+G** and ωB97XD/6-311+G** Level.

Interaction Energy (kcal/mol) BSSE-uncorrected BSSE-corrected BSSE-corrected BSSE-corrected Model

G

BG

NG

SiG

MB

M06-2X

M06-2X

B3LYP-D

ωB97XD

CAF

-26.65

-20.6

-23.8

-24.2

UA

-23.42

-18.1

-20.2

-20.0

X

-22.83

-17.5

-19.9

-19.5

HX

-21.78

-16.4

-18.9

-19.1

CAF

-24.79

-19.4

-23.8

-24.4

UA

-24.44

-19.4

-21.9

-21.5

X

-20.99

-16.4

-18.6

-18.8

HX

-20.63

-15.8

-18.4

-18.2

CAF

-27.11

-21.2

-24.3

-24.3

UA

-22.42

-17.3

-18.9

-18.8

HX

-21.14

-16.1

-18.6

-18.5

X

-20.75

-15.6

-17.6

-17.5

X

-44.93

-41.2

-39.1

-41.5

CAF

-43.87

-38.6

-37.1

-40.1

UA

-42.25

-38.5

-35.7

-38.8

HX

-30.39

-27.4

-26.9

-29.1


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


TABLE 2. Energy Decomposition Analysis of the Complexes Formed by MBs with SiG.

Complex

Ele. Stat

Orb. Int

Pau. Rep

Disp.

Inter.

Energy

Energy

Energy

Energy

Energy

(kcal/mol) (kcal/mol) (kcal/mol) (kcal/mol) (kcal/mol) SiG-CAF

-130.67

-99.48

228.79

-37.57

-38.93

SiG-HX

-135.23

-100.81

222.98

-15.27

-28.33

SiG-UA

-129.40

-103.75

228.52

-32.62

-37.25

SiG-X

-128.95

-109.12

231.53

-33.37

-39.91

Ele. Stat Energy = Electrostatic Energy, Orb. Int Energy = Orbital Interaction Energy, Pau. Rep Energy = Pauli Repulsion Energy, Disp. Energy = Dispersion Energy, Inter. Energy = Interaction Energy



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

TABLE 3. The Sum of Electron Density ρ(rc) at BCPs in the Various Complexes (a.u.).

Model

G

BG

NG

SiG

MBs

ρ(rc)

CAF

0.06

HX

0.05

UA

0.06

X

0.05

CAF

0.08

HX

0.06

UA

0.07

X

0.06

CAF

0.07

HX

0.06

UA

0.07

X

0.07

CAF

0.13

HX

0.11

UA

0.11

X

0.13


Page 28 of 49

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TABLE 4. The Laplacian of Electron Density (∇2ρ(rc)) and Total Energy Density (Hc) at BCPs of Si….O(N) Interaction (a.u.). ∇2ρ(rc)

Hc

Si…O in Si-CAF

0.09

-0.02

Si…N in Si-HX

0.07

-0.03

Si…O in Si-UA

0.10

-0.02

Si…O in Si-X

0.10

-0.02

BCP



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

TABLE 5. The Calculated Charge Transfer for Different Compexes Using NBO Analysis Employing M06-2X/ccpVDZ Method (a.u.).

Model

G

BG

NG

SiG

MBs

Charges

CAF

-0.002

HX

-0.002

UA

0.005

X

0.003

CAF

0.001

HX

0.004

UA

0.002

X

0.003

CAF

-0.001

HX

-0.002

UA

0.002

X

0.002

CAF

0.259

HX

0.230

UA

0.269

X

0.260


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


TABLE 6. The Second-order Perturbation Theory Analysis of Fock Matrix for the Complex Formed by Si-doped Graphene with MBs.

Complex SiG- CAF

SiG-HX

SiG-UA

SiG- X

Charge transfer Interaction

E(2)(kcal/mol)

BD of C-O

LP* of Si

18.42

LP of O

LP* of Si

161.63

BD of C-N

LP* of Si

14.96

BD of N-C

LP* of Si

16.85

LP of N

LP* of Si

145.94

BD of C-O

LP* of Si

14.11

LP of O

LP* of Si

150.1

BD of C-O

LP* of Si

14.78

LP of O

LP* of Si

164.6

BD is occupied orbital, LP is lone pair occupied orbital and LP* is unoccupied orbital



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

TABLE 7. The Calculated HOMO-LUMO gap for Different Compexes Using M06-2X/631+G** Method (eV). Model

MBs

HOMO-LUMO gap

G

----

4.0

CAF

4.0

HX

4.0

UA

4.0

X

4.0

----

2.4

CAF

2.4

HX

2.5

UA

2.4

X

2.4

----

2.4

CAF

2.4

HX

2.4

UA

2.4

X

2.4

----

3.7

CAF

3.6

HX

3.4

UA

3.3

X

3.3

G

BG

BG

NG

NG

SiG

SiG


Page 32 of 49

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


(i)

(i)

(ii)

(ii)

G

(i)

BG

(i)

(ii)

(ii)

NG SiG



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

CAF

HX

UA

X

Figure 1. Optimized geometries of graphene models (G, BG, NG and SiG) and MBs at M062X/6-31+G** level. (i) top view and (ii) side view.

CAF


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HX

UA

X

Figure 2. The calculated ESP isosurface of MBs (0.05 a.u)

(i)

(i)

(ii)

(ii)

3.1Å

3.2Å

G-CAF

G-HX



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

(i)

(i)

(ii)

(ii) 3.1Å

3.3Å

G-UA (i)

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G-X (i)

(ii)


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(ii) 3.3Å

3.3Å

B-CAF

B-HX

(i)

(i)

(ii)

(ii)

3.2Å

3.2Å

B-UA

B-X



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

(i)

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(i)

(ii)

(ii) 3.1Å

N-CAF (i)

3.2Å

N-HX (i)


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(ii)

(ii) 3.1Å

3.1Å

N-UA

N-X

(i)

(i)

(ii) (ii)

1.8Å 3.4Å

1.9Å

Si-CAF Si-HX



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(i)

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(i)

(ii) (ii)

1.8Å

3.2Å

3.2Å

Si-UA

1.8Å

Si-X

Figure 3. The optimized geometries of different complexes at M062X/6-31+G** level. (i) top view and (ii) side view.


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HOMO

LUMO

Figure 4. The electron density isosurafce of frontier orbitals (HOMO and LUMO) of SiG at isovalue of 0.05 a.u.



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

G-CAF

G-UA

G-HX

G-X

BG-CAF

BG-HX

BG-UA

BG-X


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NG-CAF

NG-HX

NG-UA NG-X

SiG-CAF SiG-HX



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SiG-UA

SiG-X

Figure 5. Molecular graphs of different complexes of graphene models with MBs. BCP’s are represented by red color dots.


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Si-CAF

Si-HX

Si-X

Si-UA

Figure 6. Electron density difference for the SiG-MB complexes (isovalue 0.01 a.u).



CAF SiG

HX SIG

5

5

4

DOS

DOS

4

3

3

2

2

1

1

0

0 -10

-8

-6

-4

-2

0

2

4

6

-10

-8

-6

-4

Energy(eV)

-2

0

2

4

6

Energy(eV)

UA SiG

X SiG 3.0

4

2.5

3 2.0

DOS

DOS

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

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2

1.5

1.0

1 0.5

0.0

0 -10

-8

-6

-4

-2

0

2

4

6

-10

-8

-6

-4

-2

Energy(eV)

Energy(eV)

Figure 7. PDOS of different complexes formed by SiG with MBs.


0

2

4

6

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HOMO

LUMO

Si-CAF

SiG-HX



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

SiG-UA

SiG-X

Figure 8. The isosurfaces of HOMO and LUMO electronic states of SiG-MB complexes (isovalue 0.027 a.u ).


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Table of Content (TOC)


Computational Study on the Interaction of Modified Nucleobases with

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