Applied Nanoscience

Theoretical aspects of the adsorption of normal and modified base pairs of DNA on
Graphene models toward DNA sequencing
--Manuscript Draft--

Manuscript Number:

Full Title: Theoretical aspects of the adsorption of normal and modified base pairs of DNA on
Graphene models toward DNA sequencing

Article Type: Original Article

Funding Information:

Abstract: A theoretical understanding of the adsorption of DNA base pairs (GC, AT, CAF-T &
CAF-C) on the graphene models (Gr, SiGr and SiGr-COOH) is investigated. Among
the complexes SiGr-COOH_AT is found to have the highest adsorption energies of -
202.83 kcal/mol. The strong adsorption between DNA base pairs and the SiGr-COOH
model leads to concomitant charge transfer responsible for the stability of the
corresponding models and is verified with NBO analysis. AIM analysis discloses the
high orbital overlap that signifies the strong interaction. Closed-shell interactions are
observed through the positive values of total electron density, and it is also observed
that Si-O(N) interaction has both covalent and electrostatic characteristics. UV-
absorption studies reveal the stability and binding mode of DNA with graphene models.
This is the first theoretical attempt to investigate the adsorption of DNA base pairs on
SiGr-COOH, which is more favourable than other models and may call for further
experimental studies, which is crucial in developing of new bio-sensors.

Corresponding Author: Shankar Ramasamy

Bharathiar University
INDIA

Corresponding Author Secondary

Information:

Corresponding Author's Institution: Bharathiar University

Corresponding Author's Secondary

Institution:

First Author: Radhika R

First Author Secondary Information:

Order of Authors: Radhika R

Shankar Ramasamy

Order of Authors Secondary Information:

Author Comments:

Suggested Reviewers: Pazhanivel T, Ph.D

Assistant Professor, Periyar University
pazhanit@gmail.com
Dr. Pazhanivel is from the same area of specialization.

Pitchumani Violet Mary C, Ph.D

Assistant Professor, Sri Shakthi Institute of Engineering and Technology
mviolet88@gmail.com
Dr. Pitchumani Violet Mary is expertise in density functional theory and biomolecular
interaction

Dhayal Raj A, Ph.D

Assistant Professor, Sacred Heart College
dhayalraj03@gmail.com
Dr. Dhayal Raj is from the same area of specialization.

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4 Theoretical aspects of the adsorption of normal and modified base pairs of DNA on
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Graphene models toward DNA sequencing
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10 R. Radhika, R. Shankar*
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13 * Corresponding author mail: rshankar@buc.edu.in (R. Shankar)
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4 Highlights
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8 1. The structural and electronic properties of DNA base pairs on the surface of pristine
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10 graphene (Gr), silicon-doped graphene (SiGr) and COOH functionalised Si-doped
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12 graphene (SiGr-COOH) have been investigated.
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15 2. For the first time, normal and modified base pairs of DNA adsorbed on SiGr-COOH
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17 have been observed using theoretical methods, and the outcome may call for further
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19 experimental studies.
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22 3. In the graphene models, DNA base pairs are strongly physisorbed due to the hydrogen
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24 bond, π-π stacking interactions as well as Si-O(N) interactions.
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27 4. Among the DNA adsorbed graphene models, the DNA base pairs adsorbed SiGr-COOH
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29 model is found to have the highest adsorption energy (-202.83 kcal/mol), followed by
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31 the SiGr model, which would be highly beneficial in the biosensing field.
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5 Abstract
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A theoretical understanding of the adsorption of DNA base pairs (GC, AT, CAF-T &
8 CAF-C) on the graphene models (Gr, SiGr and SiGr-COOH) is investigated. Among the
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10 complexes SiGr-COOH_AT is found to have the highest adsorption energies of -202.83
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12 kcal/mol. The strong adsorption between DNA base pairs and the SiGr-COOH model leads to
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14 concomitant charge transfer responsible for the stability of the corresponding models and is
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16 verified with NBO analysis. AIM analysis discloses the high orbital overlap that signifies the
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strong interaction. Closed-shell interactions are observed through the positive values of total
19 electron density, and it is also observed that Si-O(N) interaction has both covalent and
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21 electrostatic characteristics. UV- absorption studies reveal the stability and binding mode of
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23 DNA with graphene models. This is the first theoretical attempt to investigate the adsorption of
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25 DNA base pairs on SiGr-COOH, which is more favourable than other models and may call for
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27 further experimental studies, which is crucial in developing of new bio-sensors.
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31 Keywords: Graphene, DNA, Cancer, Targeted drug therapy, Adsorption
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6 1 Introduction
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8 Cancer is one of the greatest health threats to humans worldwide. In recent years, many
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10 treatments have been available to fight against cancer, including radiation, chemotherapy,
11 surgical resection, etc., which remain a powerful therapeutic approach against different cancers
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13 (George et al. 2013; Boys and Bernardi 1970). However, some disadvantages, such as high
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15 toxic effects and low therapeutic efficacy of chemotherapy, have limited the applications.
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17 Currently, targeted drug therapy is an important research technique used to improve drug
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19 efficacy and decrease the side effects of the drug. DNA-targeted drug therapy has drawn great
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attention in recent years since DNA is one of the major molecular targets for many anticancer
22 drugs (Hurley 2002). Since accurately detecting the specific DNA sequence amongst the whole
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24 DNA sequence is challenging, Graphene and graphene-based nanomaterials are important in
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26 DNA detection with high specificity and sensitivity (Wu et al. 2018; Heerema and Dekker
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28 2016). Graphene has attracted considerable research attention due to its exceptional mechanical,
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30 thermal, optical, transport and electronic properties (Geim and Novoselov 2007; Geim 2009;
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Novoselov et al. 2004; Balandin et al. 2008; Latil and Henrard 2006). The fascinating properties
33 of pristine graphene and its derivatives are envisaged and investigated in fields such as
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35 biomolecular sensing, energy storage, nanoelectronics and bioengineering (Xuan et al. 2008;
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37 Iyer et al. 2021; Gu et al. 2019; Pumera 2011). Graphene can be used as a carrier for DNA
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39 molecules either by π–π stacking interactions or other interactions through the functional groups
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41 of the modified graphene surface (Liu et al. 2015). Hence, in the present work, the chemical
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modification of the pristine graphene utilising atom doping and the attachment of functional
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44 group to pristine graphene aid increasing the adsorption potential of the corresponding
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46 complexes due to concomitant charge transfer (Kuila et al. 2012; Cervantes-Sodi et al. 2008;
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48 Sanyal et al. 2009). Functionalised graphene is used to differentiate the DNA nucleobases,
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50 which could be highly beneficial in DNA sequencing (Prasongkit et al. 2013). Hence to
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52 improve the intermolecular interactions, it is preferred to functionalise the graphene with the
53 carboxyl group that contributes to the fabrication of efficient bio-sensor devices (Sun et al.
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55 2017). From the literatures, it is observed that even though hydroxyl, carboxylic and alkyl
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57 groups could be used for the functionalisation process in graphene, COOH functional group is
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59 chosen for its versatility which is considered the best in functionalisation with the biomolecules
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4 (Prato et al. 2017; Ménard-Moyon et al. 2016). Huang et al. synthesised carboxylic acid-
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6 functionalised graphene to detect guanine and adenine electrochemically (Huang et al. 2011).
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8 Chemical groups can be attached to graphene through two different configurations: defect
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10 functionalisation and group-terminated configuration. However, the defects are considered
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12 toxic, limiting the bio-application (Fenoglio et al. 2008). The graphene nano ribbons doped with
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the boron-nitrogen showed different transmission signals for the nucleobases (Bhattacharya et
15 al. 2015; Song et al. 2012).
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17 In the pristine graphene (Gr) various atoms such as nitrogen, boron, phosphorus, silicon
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19 and sulfur are being used to change the electron density and thus could be used in many
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21 applications (Zhang et al. 2015). Due to the high biocompatibility and high adsorption energy
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23 of silicon-doped graphene with DNA, it was found appealing one in the biosensing field (Ye et
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al. 2013). Previous experimental reports strongly support the occurrence of the Si atom in the
26 graphene lattice along with their corresponding electronic structure and nature of the chemical
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28 bonding (Zhou et al. 2012; Chisholm et al. 2012). A recent study reveals the possible
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30 application of silicene (silicon as a reactive center) as a biosensor, in which guanine and
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32 cytosine are weakly chemisorbed through the Si-O bond. In contrast, adenine and thymine are
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34 physisorbed on silicene which prompted us to study more on silicon doped graphenes (SiGr)
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(Amorim and Scheicher 2015). The enhanced sensing properties of SiGr than graphene inspire
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37 us to deal with the SiGr (Lv et al. 2014; Zou et al. 2011; Chen et al. 2012). Since, the interaction
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39 between the functionalised graphene and the biomolecules is more favorable than pristine
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41 graphene due to the presence of hydrophilic groups, the surface of the Si-doped graphene is
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43 functionalised with the COOH group (SiGr-COOH) in the present work (Lounasvuori et al.
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45 2014; Liu et al. 2012). This work uses pristine graphene, Si-doped graphene and Si-doped
46 graphene functionalised with COOH as model systems that could effectively interact with DNA
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48 base pairs and may assist in developing the sensor. In addition to the normal DNA base pairs
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50 GC and AT, some modified base pairs exist in our body, such as uric acid, caffeine, xanthine
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52 and hypoxanthine (Yamamoto et al. 2005). The modified nucleobase caffeine is a
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54 methylxanthine that enters the body with coffee, tea and coca-cola (Biaggioni et al. 1991). It is
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56 a sensitive indicator for several pathological states, including diuresis, gastric acid secretion and
57 stimulation of the central nervous system (Spãtaru et al. 2002; Graham 1978). Many research
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59 works have investigated the association between caffeine and cancer risk, and the results are
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4 inconsistent. Some studies of caffeine revealed an increased risk of cancer, and few studies
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6 indicate decreased risk of cancer or no effect on cancer (Ganmaa et al. 2008; Vatten et al. 1990;
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8 Xie et al. 2016). Saito et al. revealed that the combined treatment with Ad-PTEN and caffeine is
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10 a potential therapy for colorectal cancer (Saito et al. 2003). Hence, caffeine detection in body
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12 fluids is important for clinical diagnosis. Since caffeine is a purine analogue, it could be paired
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with Thymine (T) or Cytosine (C) (Ebrahimi et al. 2013). Hence, in this study, modified
15 nucleobase pairs Caffeine-Thymine (CAF-T) and Caffeine- Cytosine (CAF-C) are used along
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17 with the normal DNA base pairs. The earlier investigation shows that the electrodes developed
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19 from carbon and multi-walled carbon nanotubes were used to detect modified nucleobases
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21 (Wang et al. 2003; Kang et al. 2009). Alwarappan et al. concluded that graphene electrodes
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23 exhibit superior performance than carbon nanotubes (Alwarappan et al. 2009). Swathi et al.
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revealed the theoretical aspects of the nucleobases with the graphyne and graphdiyne to
26 understand the phenomena of nanobio interface that strongly supports the strength of DNA
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28 adsorption on graphene, which is useful in electrochemical detection (Chandra Shekar and
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30 Swathi 2014). Hence, the theoretical aspect of the molecular-level interaction between the
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32 normal and modified DNA base pairs and graphene has become the basis for developing new
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34 sensors. To the best of our knowledge, no theoretical studies in the literature explore the
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interaction of DNA normal and modified base pairs with the Si-doped graphene and COOH-
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37 functionalised Si-doped graphene models. In this investigation, an attempt is made to explore
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39 the interaction of normal (GC & AT) and modified(CAF-T &CAF-C) DNA base pairs with
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41 pristine graphene, Si-doped graphene and COOH-functionalised Si-doped graphene. The
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43 mechanism of pristine graphene, Si-doped graphene and chemical functionalisation of Si-doped
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45 graphene by the COOH group is investigated to analyse the structural and electronic properties.
46 These findings are believed to shed light on understanding the nanobio interface. These studies
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48 reveal the potential applications of DNA sequencing, which will be beneficial in making
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50 personalised medicine in cancer therapy (Ferrari 2005; Mudedla et al. 2014).
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54 2 Computational details
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56 Initially, the structures of Gr, SiGr and SiGr-COOH, isolated DNA normal base pairs
57 (GC and AT) and modified base pairs (CAF-T and CAF-C) were optimised using the M06-
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59 2X/6-31+G** level of theory. The DNA base pairs were then adsorbed with the pristine
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4 graphene, Si-doped graphene, and COOH-functionalised Si-doped graphene were optimised at
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6 the same level of theory. In the adsorption energy calculation, a three-body analysis was used to
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8 get deep insights into the DNA adsorbed graphene models.To visualise the electronic transport
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10 properties and charge distributions HOMO & LUMO have been plotted (Reed et al. 1985).
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12 Reduced Density Gradient (RDG) analysis (Johnson et al. 2010) was evaluated by the wave
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function analysis program of Multiwfn 3.5 (Lu and Chen 2012), and the Non-Covalent
15 Interaction (NCI) isosurfaces were plotted by VMD 1.9.3 program to examine the nature of the
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17 hydrogen bonds (Humphrey et al. 1996). UV–Vis spectrum was plotted to observe the stability
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19 and binding mode of DNA with the graphene models (Maitra 2016). Further, to investigate the
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21 sensitivity of DNA base pairs towards the adsorption of graphene models, Partial density of
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23 states (PDOS) was observed using GaussSum 3.0 program.(Fenoglio et al. 2008)
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26 3 Results and discussion
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28 3.1 Structural deformation study
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30 The main objective of this study is to observe the interactions of the normal (GC and
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32 AT) and modified DNA base pairs (CAF-T and CAF-C) with the graphene models (Gr, SiGr
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34 and SiGr-COOH). The C42H16 molecule is used as a model system for pristine graphene. The
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pristine graphene is doped with Si-atom, and the dopant position selection follows the work of
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37 Mudedla et al. (Mudedla et al. 2014). Since it is observed from the earlier studies that the
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39 density functional M06-2X is used to find the interaction studies of DNA with graphene, the
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41 same functional is used in the present work (Zhao et al. 2006; Umadevi and Sastry 2011). The
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43 normal DNA base pairs (GC and AT) were taken from Protein Data Bank (PDB ID: 1BNA)
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45 (Drew et al. 1981). Initially, isolated DNA base pairs and graphene models are optimised by the
46 M06-2X/6-31+G(d,p) method. The DNA base pairs adsorbed with the pristine graphene
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48 (Gr_AT, Gr_GC, Gr_CAF-C and Gr_CAF-T), Si-doped graphene (SiGr_AT, SiGr_GC,
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50 SiGr_CAF-C and SiGr_CAF-T) and COOH-functionalised Si-doped graphene (SiGr-
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52 COOH_AT, SiGr-COOH_GC, SiGr-COOH_ CAF-C and SiGr-COOH_ CAF-T) were
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54 optimised at the same level of theory and are shown in Fig. 1 and Fig. 2. The suitability of the
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56 method M06-2X/6-31+G(d,p) is confirmed by the previous literature (Zhao and Truhlar 2008;
57 Radhika et al. 2017). To confirm whether the structures are on the real minima, vibrational
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59 frequency calculations are carried out for the above models at the same level of theory.
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4 In the isolated graphene model systems as well as DNA base pairs adsorbed model
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6 systems, all the C-C bonds are of sp2-sp2 types. Due to the aromatic character of DNA, the
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8 interactions with the graphene models are primarily governed by π-π stacking along with the
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10 hydrogen bonds, partial electrostatic and covalent bonds that play an important role in the
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12 stabilisation of the complexes. Table 1 shows that in both SiGr and SiGr-COOH graphene
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models, the Si-C bond is perturbed and adopts the concave shape with the values of 1.732 to
15 1.776 Å and 1.743 to 1.783 Å, which is larger than the normal Si-C bond (1.420 Å). Thus Si-
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17 atom protrudes from the graphene plane and preserves its sp3 character due to its large atomic
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19 size which introduces curvature around Si atom in the graphene surface, which is in agreement
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21 with the earlier reports (Mudedla et al. 2014; Chen et al. 2013). The DNA base pairs stacked
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23 with the graphene models through π-π interaction with the vertical rise of 3.260 to 5.990 Å. It is
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observed that the distance of the stacking interactions is found to be in the range of 3.260 to
26 5.290 Å, 3.260 to 5.980 Å and, 3.300 to 5.990 Å for DNA base pairs adsorbed graphene models
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28 of pristine graphene, SiGr and SiGr-COOH, respectively. The hydrogen bond interactions are
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30 found to be in the range of 1.478 to 3.080 Å, in which the interactions of DNA with the pristine
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32 graphene, SiGr and SiGr-COOH graphene models are in the range of 1.755 to 2.743 Å, 1.550 to
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34 2.870 Å and 1.478 to 3.080 Å respectively. In addition, bond length values of the covalent bond
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interactions (Si…O and Si…N) are in the range of 1.763 to 1.993 Å.
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37 Thus the adsorption between DNA base pairs and graphene models is governed
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39 by π-π stacking, hydrogen bond and covalent bond interactions. In the hydrogen bond
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41 interactions, both conventional (N-H…N, N-H…O, and O-H…O) and nonconventional
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43 (C-H…O and C-H…N) intermolecular hydrogen bonds are observed. The complexes are
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45 stabilised with twenty N-H…O bonds, six N-H…N bonds, four O-H…O bonds, eleven C-
46 H…O bonds and two C-H…N bonds. Since the structural parameters plays a vital role in the
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48 chemical properties, bond length and bond angle values were elaborately discussed. The
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50 structural parameters are shown in Table 1, and the values of hydrogen bond length and
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52 hydrogen bond angle are in the ranges between 1.478 and 3.065 Å as well as 91.6º and 178.2º,
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54 respectively. The hydrogen bond lengths, as well as bond angles, are observed to be in the
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56 range of 1.755 to 2.744 Å, 1.551 to 2.595 Å and 1.478 to 3.065 Å as well as 135.0 to 178.2º,
57 127.0 to 175.1º and 91.6 to 175.8º for the DNA base pairs adsorbed graphene models of pristine
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59 graphene, SiGr and SiGr-COOH respectively.
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13 GC AT
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40 Gr SiGr
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55 SiGr-COOH
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57 Fig. 1 Optimised structures of isolated DNA normal and modified base pairs
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60 and graphene models
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Gr_GC
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39 SiGr-COOH_GC
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56 Fig. 2(a) Optimised structures of GC base pairs with Gr, SiGr and SiGr-COOH
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Gr_AT
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39 SiGr-COOH_AT
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57 Fig. 2(b) Optimised structures of AT base pairs with Gr, SiGr and SiGr-COOH
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Gr_CAF-C
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40 SiGr-COOH_CAF-C
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56 Fig. 2(c) Optimised structures of CAF-C base pairs with Gr, SiGr and SiGr-COOH
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55 Fig. 2(d) Optimised structures of CAF-T base pairs with Gr, SiGr and SiGr-COOH
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4 Table 1 Structural parameters, hydrogen bond stabilisation energies E(2) and occupation number
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6 of the acceptor lone pair n(y) & proton donor σ* (X-H) calculated at M062X/cc-pVDZ
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9 hydrog
hydro X-H ( ) X-H…X (°) N(Y) a.u σ*(X-H)
10 en E(2)
gen
11 Bonding bond
bond
Type angle kcal/
12 length Complex Monomer Complex Monomer Complex Monomer Complex Monomer
mol
13 ( ) (°)
14 Gr_GC
15 N4-H4a…O6 1.755 175.800 1.032 1.034 119.300 120.000 1.863 1.862 0.059 0.055 9.4
16 N2-H2a…O2 1.870 174.700 1.022 1.020 120.900 122.800 1.860 1.860 0.038 0.035 10.0
17 N1-H1…N3 1.875 173.600 1.036 1.033 119.700 119.100 1.865 1.870 0.060 0.059 19.9
18 Gr_AT
19 N6-H6a…O4 1.889 171.300 1.021 1.020 120.000 120.500 1.875 1.875 0.038 0.034 9.0
20 N3-H3…N1 1.756 178.200 1.050 1.053 116.600 115.700 1.860 1.861 0.059 0.085 30.8
C2-H2…O2 2.744 135.000 1.089 1.088 117.300 117.400 1.851 1.851 0.025 0.025 0.4
21
Gr_CAF-C
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N4-H4a…O6 1.953 167.300 1.017 1.018 116.500 118.700 1.959 1.960 0.026 0.028 9.7
23 C1-H1a…N3 2.316 150.400 1.089 1.086 111.400 110.300 1.889 1.891 0.018 0.017 4.4
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Gr_CAF-T
25 N3-H3…O2 1.821 169.200 1.024 1.026 116.400 116.000 1.951 1.955 0.049 0.041 16.6
26 C3-H3a…O4 2.342 144.800 1.091 1.090 111.000 111.000 1.873 1.875 0.014 0.009 1.5
27 SiGr_GC
28 N4-H4a…O6 1.900 175.100 1.026 1.034 120.400 120.000 1.858 1.862 0.041 0.055 9.3
29 N1-H1…N3 1.761 173.300 1.049 1.033 118.900 119.100 1.850 1.870 0.067 0.059 28.3
30 N2-H2a…O2 1.551 166.100 1.081 1.020 116.000 122.800 1.844 1.860 0.044 0.035 13.2
31 SiGr_AT
32 N6-H6a…O4 1.998 171.300 1.020 1.020 120.100 120.500 1.874 1.875 0.032 0.034 6.1
33 N3-H3…N1 1.811 166.600 1.042 1.053 114.900 115.700 1.866 1.861 0.080 0.085 32.0
C2-H2…O2 2.595 127.000 1.089 1.088 117.300 117.400 1.853 1.851 0.025 0.025 0.5
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35 SiGr_CAF-C
N4-H4a…O6 2.061 149.300 1.016 1.018 117.900 118.700 1.950 1.960 0.021 0.028 5.6
36 C1-H1a…N3 2.282 155.000 1.086 1.086 110.000 110.300 1.882 1.891 0.018 0.017 4.6
37
SiGr_CAF-T
38 N3-H3…O2 1.701 154.900 1.040 1.026 117.900 116.000 1.941 1.955 0.039 0.041 11.8
39
SiGr-COOH_AT
40 N6-H6a…O4 2.017 175.800 1.023 1.020 121.600 120.500 1.879 1.875 0.034 0.034 5.4
41 N3-H3…N1 1.047 170.428 1.768 1.750 111.259 115.724 1.847 1.861 0.079 0.085 31.8
42 C2-H2…O2 2.662 120.600 1.087 1.088 120.100 117.400 1.894 1.851 0.021 0.025 0.3
43 O9-H11…O4 1.798 171.500 0.987 0.968 112.600 112.600 1.946 1.875 0.045 0.008 10.3
44 N6-H6b…O12 2.070 138.100 1.019 1.008 116.987 118.878 1.968 1.975 0.022 0.007 3.3
45 N9-H9…O15 2.051 142.900 1.021 1.009 125.476 125.809 1.966 1.974 0.032 0.018 3.6
C8-H8…O14 2.680 91.600 1.081 1.082 121.422 121.537 1.971 1.972 0.016 0.018 0.2
46
47 SiGr-COOH_GC
N2-H2a…O2 1.478 168.900 1.109 1.020 115.303 122.814 1.959 1.963 0.034 0.035 7.6
48 N1-H1…N3 1.765 175.500 1.048 1.033 119.391 119.065 1.850 1.870 0.086 0.059 34.5
49 N4-H4a…O6 1.937 174.000 1.025 1.034 120.176 120.025 1.858 1.862 0.039 0.007 8.6
50 N9-H9…O18 2.260 127.600 1.016 1.009 124.547 127.760 1.842 1.974 0.025 0.018 2.1
51 C8-H8…O18 3.065 96.600 1.081 1.081 121.212 121.529 1.970 1.974 0.018 0.020 0.2
52 C8-H8…O13 2.627 106.500 1.081 1.081 121.212 121.529 1.973 1.975 0.018 0.020 0.2
53 N4-H4b…O3 2.081 146.700 1.015 1.007 119.653 120.387 1.851 1.853 0.023 0.007 3.8
54 SiGr- COOH_CAF-C
55 C8-H8…O6 2.426 130.300 1.084 1.082 124.401 124.736 1.971 1.967 0.019 0.018 0.9
C3-H3c…O4 2.689 149.400 1.091 1.089 110.533 110.535 1.971 1.849 0.009 0.007 0.4
56
C3-H3b…O19 2.634 130.600 1.089 1.092 108.787 109.781 1.852 1.974 0.010 0.010 0.6
57 N1-H1…O10 2.410 144.700 1.016 1.010 115.914 115.244 1.850 1.967 0.026 0.016 1.4
58 N4-H4b…O14 2.330 139.100 1.013 1.005 119.329 121.070 1.845 1.975 0.015 0.007 1.7
59 SiGr-COOH_CAF-T
60 N3-H3…O2 2.025 140.900 1.028 1.026 118.750 116.005 1.962 1.955 0.033 0.041 5.6
61 C3-H3b…O4 2.513 95.900 1.091 1.091 109.414 110.394 1.909 1.916 0.010 0.011 0.1
62 O17-H29…O6 1.736 171.700 0.987 0.970 111.086
14 107.690 1.950 1.876 0.048 0.012 13.6
63 O10-H25…O2 2.151 150.700 0.973 0.968 113.003 112.585 1.851 1.975 0.024 0.008 3.0
64 O12-H26…O2 2.064 141.600 0.972 0.976 111.876 112.069 1.963 1.849 0.019 0.007 3.8
65
 1
2
3
4 In addition, bond elongation and contraction are found to be in the range of 0.001 to
5
6 0.703 Å for the hydrogen bond length and 0.1 to 7.5º for the hydrogen bond angle in the DNA
7
8 base pairs adsorbed graphene models. Especially the structural changes are found to be in the
9
10 range of 0.001 to 0.003 Å, 0.001 to 0.061 Å and 0.001 to 0.703 Å (bond length) and 0.1 to 2.2º,
11
12 0.1 to 6.8 º and 0.1 to 7.5º (bond angle) for DNA base pairs adsorbed pristine graphene, SiGr
13
14
and SiGr-COOH respectively. Among the various models, DNA base pairs adsorbed SiGr-
15 COOH have high structural deformations with high adsorption energies. Especially in the bond
16
17 N3-H3…N1, the highest contraction of 0.703 Å is observed in the proton donor N3-H3 with the
18
19 angle deviation of 6.7º compared with the isolated DNA basepairs in the SiGr-COOH_AT
20
21 complex with the high adsorption energy of -202.8 kcal/mol and the occupancy of proton donor
22
23 N3-H3 is obtained as 0.079 a.u which is decreased by 0.006 a.u than its isolated DNA basepair
24
25
value (0.085 a.u). Thus the higher charge transfer in the corresponding bonds leads to strong
26 adsorption energy, resulting in high structural deviations. In the complex SiGr-COOH_GC, the
27
28 proton donor N2-H2a is found to be highly elongated by 0.089 Å in the bond N2-H2a…O2
29
30 with the bond angle deviation of 7.5º with the adsorption energy of -97.4 kcal/mol and the
31
32 occupancy value of the antibonding donor N2-H2a is found to be 0.034 a.u which is decreased
33
34 from its corresponding monomer value by 0.001 a.u. Among the DNA base pairs adsorbed
35
SiGr, SiGr_GC deviation of 6.8° in the bond N2-H2a…O2 with the corresponding bond length
36
37 deviation of 0.067 Å with the adsorption energy of -67.7 kcal/mol and the occupancy values of
38
39 the antibonding donor N2-H2a is 0.044 a.u with the monomer value of 0.035 a.u. DNA base
40
41 pair adsorbed pristine graphene is found to have low structural deformations that results from
42
43 low adsorption energies. These structural changes will be substantiated through NBO analysis.
44
45 Among the various models, DNA base pairs adsorbed SiGr-COOH have high structural
46 deformation, specifically in the active sites of carbonyl, amine and amide groups. These
47
48 structural deviations stabilise the corresponding complexes, leading to better adsorption energy
49
50 between DNA base pairs and graphene models.
51
52
53
54 3.2 Adsorption energy
55
56 The adsorption energy is calculated for isolated DNA base pairs and DNA base pair
57 adsorbed graphene models using the counterpoise method to eliminate the BSSE. These are
58
59 given in Table 2.
60
61
62 15
63
64
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 1
2
3
4 The order of adsorption energy of the isolated base pairs is GC > AT >CAF-T > CAF-C
5
6 with the adsorption energies of 30.75, -15.79, -7.89 and -7.68 kcal/mol, respectively. In the
7
8 event of isolated base pairs, the adsorption energy of GC is observed with the highest value of
9
10 -30.75 kcal/mol. These results well agreed with the previous outcome. (Ebrahimi et al. 2013;
11
12 Radhika et al. 2017; Chen et al. 2013; Deepa et al. 2008; Shankar et al. 2015) Among the DNA
13
14
adsorbed graphene models, the DNA base pairs adsorbed SiGr-COOH model has the highest
15 adsorption energy of -202.83 kcal/mol, whereas Gr-CAF-T is observed as the least adsorption
16
17 energy of -31.32 kcal/mol.
18
19
20
21 The order of adsorption energy is given below:
22
23 SiGr-COOH_AT > SiGr-COOH_GC > SiGr-COOH_CAF-C > SiGr-COOH_CAF-T > SiGr-
24
25
GC > Gr_GC > SiGr_CAF-T > Gr-AT > SiGr_AT > SiGr_CAF-C > Gr_CAF-C > Gr_CAF-T
26
27
28 In the case of DNA adsorbed pristine graphene models, Gr-GC shows the highest
29
30 adsorption energy of -55.07 kcal/mol, followed by the second highest adsorption energy of
31
32 -37.79 kcal/mol for the Gr-AT complex. Based on the size of the graphene sheets, the
33
34 adsorption energy of Gr-GC and Gr-AT are found to be in the range of -49.9 to -72.6 kcal/mol
35
and -34.7 to -55.1 kcal/mol respectively (Jens Antony and Stefan Grimme 2008). The lowest
36
37 adsorption energies of -33.6 and -31.3 kcal/mol are observed for the Gr-CAF-C and Gr-CAF-T
38
39 complexes, respectively. While considering the DNA adsorbed SiGr and SiGr-COOH models,
40
41 the adsorption energies are significantly higher than DNA adsorbed pristine graphene model.
42
43 The order of adsorption energy is found to be SiGr-GC (-67.73 kcal/mol) >
44
45 SiGr_CAF-T (-52.60 kcal/mol) > SiGr_AT (-36.83 kcal/mol) > SiGr_CAF-C (-35.00
46 kcal/mol). In the DNA adsorbed SiGr-COOH models, the SiGr-COOH_AT complex
47
48 demonstrates the highest adsorption energy of -202.82 kcal/mol, followed by the higher
49
50 adsorption energy of -97.36, -88.95 and -86.44 kcal/mol for the complexes SiGr-COOH_GC,
51
52 SiGr-COOH_CAF-C, SiGr-COOH_CAF-T, respectively. Many studies suggest the trend for
53
54 the order of the adsorption energy of DNA on graphene as Guanine > Adenine > thymine >
55
56 cytosine, while those of DNA base pairs follow the order as GC > AT (Sun et al. 2017; Chandra
57 Shekar and Swathi 2014).
58
59
60
61
62 16
63
64
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 1
2
3
4 Table 2 The adsorption energy of DNA adsorbed graphene complexes
5
6
7
8 Adsorption energy Available literature value
Complex
9 (kcal/mol) (kcal/mol)
10
11 Gr_AT
12 ∆²E (iso) -15.79 -12.9 a -12.6 b
13 ∆E (Tot) -37.79 -34.7 to -55.1 d
14 ∆²E(Gr+A) -9.69
15
∆²E(Gr+T) -12.54
16
17 ∆²E (AT) -15.66
18 ∆³E 0.10
19 Gr_GC
20 ∆²E (iso) -30.75 -27.9 a -26.5 b
21
22 ∆E (Tot) -55.07 -49.9 to -72.6 d
23 ∆²E(Gr+G) -15.01
24 ∆²E(Gr+C) -11.23
25 ∆²E (GC) -30.62
26 ∆³E 1.79
27
28 Gr_CAF-C
29 ∆²E (iso) -7.68 -5.3 to -9.3 c
30 ∆E (Tot) -33.64
31 ∆²E(Gr+ CAF) -15.59
32 ∆²E(Gr +C) -11.36
33
∆²E (CAF+C) -6.81
34
35 ∆³E 0.12
36 Gr_CAF-T
37 ∆²E (iso) -7.89 -5.9 to ˗ 8.6 c
38 ∆E (Tot) -31.32
39
∆²E(Gr+ CAF) -11.31
40
41 ∆²E(Gr+ T) -12.30
42 ∆²E (CAF+T) -7.78
43 ∆³E 0.08
44 SiGr_AT
45
∆²E (iso) -15.79 -12.9 a -12.6 b
46
47 ∆E (Tot) -36.83
48 ∆²E(SiGr+A) -9.98
49 ∆²E(SiGr+T) -11.75
50 ∆²E (AT) -14.70
51 ∆³E -0.40
52
53 SiGr_GC
54 ∆²E (iso) -30.75 -27.9 a -26.5 b
55 ∆E (Tot) -67.73
56 ∆²E(SiGr+G) -14.06
57 ∆²E(SiGr+C) -11.54
58
∆²E (GC) -25.00
59
60 ∆³E -17.13
61
62 17
63
64
65
 1
2
3
4 SiGr_CAF-C
5
6 ∆²E (iso) -7.68 -5.3 to -9.3 c
7 ∆E (Tot) -35.00
8 ∆²E(SiGr+ CAF) -17.21
9 ∆²E(SiGr +C) -10.34
10 ∆²E (CAF+C) -6.29
11 ∆³E -1.15
12
13 SiGr_CAF-T
14 ∆²E (iso) -7.89 -5.9 to ˗ 8.6 c
15 ∆E (Tot) -52.60
16 ∆²E(SiGr+ CAF) -12.99
17
∆²E(SiGr+ T) -12.99
18
19 ∆²E (CAF+T) -6.13
20 ∆³E -20.49
21 SiGr-COOH_AT
22 ∆²E (iso) -15.79 -12.9 a -12.6 b
23
∆E (Tot) -202.83
24
25 ∆²E(SiGr-COOH +A) -19.24
26 ∆²E(SiGr-COOH +T) -60.62
27 ∆²E (AT) -100.91
28 ∆³E -22.05
29
30 SiGr-COOH_GC
31 ∆²E (iso) -30.75 -27.9 a -26.5 b
32 ∆E (Tot) -97.36
33 ∆²E(SiGr-COOH +G) -31.83
34 ∆²E(SiGr-COOH +C) -19.05
35 ∆²E (GC) -25.31
36
∆³E -21.17
37
38 SiGr-COOH_CAF-C
39 ∆²E (iso) -7.68 -5.3 to -9.3 c
40 ∆E (Tot) -88.95
41 ∆²E(SiGr-COOH + CAF) -59.02
42
43 ∆²E(SiGr-COOH + C) -23.31
44 ∆²E (CAF+C) -2.23
45 ∆³E -4.40
46 SiGr-COOH_CAF-T
47
∆²E (iso) -7.89 -5.9 to ˗ 8.6 c
48
49 ∆E (Tot) -86.44
50 ∆²E(SiGr-COOH + CAF) -24.22
51 ∆²E(SiGr-COOH + T) -53.57
52 ∆²E (CAF+T) -7.53
53 ∆³E -1.12
54
55 ∆²E (iso) = isolated DNA base pair, ∆E (Tot) = total adsorption energy of graphene adsorbed DNA,
56
57
∆²E (Gr+G) = interaction energy of Guanine base pair with graphene and similar for other cases
58 and ∆³E =many body interaction energy (a: Deepa et al., b: Sponer et al., c: Ebrahimi et al., d:
59 Antony et al.)
60
61
62 18
63
64
65
 1
2
3
4 To the controversy of the above observation, SiGr-COOH_AT is found to have the
5
6 highest adsorption energy (-202.83 kcal/mol), and the same trend was observed earlier (Das et
7
8 al. 2008; Zhao 2011). The increased adsorption energies in the SiGr-COOH model arise due to
9
10 Si…O(N) and π-π stacking interactions. The strong interaction of Si and O(N) arises as the
11
12 electrophilic nature of the Si atom is considerably higher than its nucleophilic character. In the
13
14
case of isolated base pairs, two body adsorption energies are found to be slighter
15 higher (0.10 to 5.75 kcal/mol) than the corresponding base pairs in the DNA adsorbed graphene
16
17 models in the absence of graphene because of the new hydrogen bonds formed between the
18
19 DNA base pairs and graphene models. The two-body adsorption energies of the isolated AT,
20
21 GC, CAF-C and CAF-T DNA base pairs are observed to be -15.79, -30.75, -7.68 and -7.89
22
23 kcal/mol while during the adsorption of the corresponding base pairs with the pristine graphene,
24
25
SiGr graphene and SiGr-COOH graphene and in the absence of graphene models adsorption
26 values of those corresponding nucleobase pairs are observed to be -15.66,-30.62, -6.81 and -
27
28 7.78 (pristine graphene), -14.70, -25.00, -6.29 & -6.13 (SiGr) and -100.91,-25.31, -2.23 and -
29
30 7.53 kcal/mol (SiGr-COOH). Notably, in the case of SiGr-COOH_AT, is
31
32 significantly higher (-100.91 kcal/mol) than the iso base pairs that strongly support the
33
34 maximum stability of that complex with the highest adsorption energy. While comparing two
35
36 body adsorption energies of all the complexes, DNA adsorbed SiGr-COOH models are
37 observed with higher energies for the complexes SiGr-COOH_AT (-19.24 and -60.62
38
39 kcal/mol), SiGr-COOH_GC (-31.83 and -19.05 kcal/mol), SiGr-COOH_CAF-C (-59.01 and -
40
41 23.31 kcal/mol) and SiGr-COOH_CAF-T (-24.22 and -53.57 kcal/mol). Positive values of the
42
43 three-body interaction energies for the DNA adsorbed pristine graphene represents the lower
44
45 adsorption values in the corresponding complexes.
46
47
In the case of DNA adsorbed SiGr complexes, slightly higher negative values for the
48 three-body interaction have been observed due to the increased interaction energy than the
49
50 pristine graphene. Among the complexes, DNA adsorbed SiGr-COOH complexes show the
51
52 highest negative three-body interaction energies, in which SiGr-COOH_AT is observed with
53
54 the highest negative value of -22.05 kcal/mol that arises due to the strong interaction followed
55
56 by the energy values of -21.17, -4.40 and -1.12 kcal/mol for the complexes SiGr-COOH_GC,
57
58
SiGr-COOH_CAF-C and SiGr-COOH_CAF-T, respectively. From these results, it is observed
59 that the adsorption between DNA base pairs with SiGr and SiGr-COOH complexes is found to
60
61
62 19
63
64
65
 1
2
3
4 be higher than pristine graphene. The DNA base pair GC is found to have high adsorption
5
6 energies with the pristine graphene and SiGr complexes with the values of -55.07 and -67.73
7
8 kcal/mol, whereas AT base pair is absorbed well with the SiGr-COOH complex (-202.83
9
10 kcal/mol). The carboxyl group in the SiGr-COOH interacts well with the AT base pair than the
11
12 GC base pair. Moreover, it is observed that the highest adsorption energy is obtained not only
13
14
by the number of hydrogen bonds but also by the strength of hydrogen bonds, confirmed by the
15 Natural bond orbital analysis (Hobza and Sponer 1999; Loza-Mejía et al. 2009). Among the
16
17 graphene models, SiGr-COOH is found to have the highest adsorption energy with the DNA
18
19 base pairs, which could be highly beneficial in DNA sensing. To understand the intrinsic
20
21 interaction (without any external effects) of DNA adsorbed graphene models, quantum
22
23 chemical studies in the gas phase are used, which can be utilised in force field development.
24
25
The adsorption studies show that SiGr-COOH followed by SiGr are found to be adsorbed well
26 with the DNA base pairs, which could be beneficial in bio-sensing applications.
27
28
29
30 3.3 Reduced density gradient (RDG) map
31
32 RDG map is plotted for DNA base pairs adsorbed graphene models to examine the
33
34 variation from distribution of homogeneous electrons, widely used to provide detailed analysis
35
for closed-shell interaction (Contreras-Garcia et al. 2011).
36
37
38 RDG =
39
40
41 In the above equation, ‘ρ’ represents the electron density and ‘ ρ’represents the norm of the
42 energy density gradient vector. The isosurface of RDG is a valuable tool for observing the more
43
44 intuitive picture of hydrogen bonds, van der Waals interactions and steric repulsions. RDG was
45
46 plotted with the Multiwfn program (Lu and Chen 2012) as a function of sign (λ2)ρ, and the NCI
47
48 isosurfaces were visualised with VMD code (Humphrey et al. 1996). RDG map along with NCI
49
50 isosurfaces have been presented in Fig. 3.
51
52
In the RDG map, the spikes at large negative values of (λ2)ρ reveal the non-covalent
53 interactions (hydrogen bond and van der Walls). In contrast, non-bonded interactions are
54
55 identified with the spike at large positive values, and the covalent bond is represented by the
56
57 spike near zero. The NCI isosurfaces are observed with red, green and blue colors to
58
59 characterise the strong repulsive interactions, weak attractive interactions and strong attractive
60
61
62 20
63
64
65
 1
2
3
4 interactions, respectively. In the case of DNA adsorbed pristine graphene models, blue color
5
6 isosurfaces have been observed in the hydrogen bonds N3-H3…N1 and N6-H6a…O4 (Gr_AT),
7
8 N2-H2a…O2, N1-H1…N3 and N4-H4a…O6 (Gr_GC) as well as N3-H3…O2 (Gr_CAF-T)
9
10 that represents the strong hydrogen bond interactions in those molecules. Whereas the
11
12 remaining hydrogen bonds in those molecules C2-H2…O2 (Gr_AT), N4-H4a…O6 and C1-
13
14
H1a…N3 (Gr_CAF-C) as well as C3-H3a…O4 (Gr_CAF-T) are witnessed by the green colour
15 isosurfaces resulting from the weak hydrogen bonds.
16
17 At the same time, the steric effect in the benzene rings and the stacking interactions
18
19 have been represented by red and green mixed brownish color isosurfaces. Due to the strong
20
21 hydrogen bonds in the complex Gr_GC, the low gradient troughs and low-density spikes are
22
23 observed in the negative region of -0.029 to -0.035 a.u which arises due to high adsorption
24
25
energy. In addition, troughts are obtained with the large and positive values in sign (λ2)ρ that
26 correspond to the steric effect in the benzene rings that are represented by red in color as well as
27
28 spikes were observed in the center of the RDG map by green mixed brownish color isosurfaces
29
30 that represent the stacking interactions between the graphene and GC base pair.
31
32 For the complexes, Gr_AT, Gr_CAF-C and Gr_CAF-T, spikes have been observed in
33
34 the range of 0.027 a.u, -0.010 to -0.020 a.u and -0.015 to -0.027 a.u. respectively. While
35
comparing DNA adsorbed SiGr models, SiGr_GC is observed with two troughs in the negative
36
37 region (-0.028 and -0.046 a.u.) with the corresponding blue region in the isosurface for the
38
39 hydrogen bonds N1-H1…N3 and N2-H2a…O2 that denotes the strong adsorption in the
40
41 complex. In addition, weak hydrogen bonds are observed in the hydrogen bond N4-H4a…O6.
42
43 Thus, in the SiGr_CAF-T, SiGr_CAF-C and SiGr_AT complexes, troughs are observed in the
44
45 range of -0.014 to -0.042 a.u, -0.012 to -0.018 a.u and -0.012 to -0.042 a.u. respectively,
46 inwhich the strong hydrogen bonds N1-H1…N3 and N2-H2a…O2 (SiGr_GC), N3-H3…O2
47
48 (SiGr_CAF-T) and N3-H3…N1 (SiGr_AT) were indicated by the blue colour regions and the
49
50 remaining weak hydrogen bonds in those complexes were observed with the green colour
51
52 isosurfaces. Likewise, the steric and stacking interactions in the DNA adsorbed SiGr complexes
53
54 are witnessed by the red and green mixed brownish color isosurfaces. In the case of DNA
55
56 adsorbed SiGr-COOH complexes, SiGr-COOH_AT is found to have the blue colour regions at
57 the bonds N3-H3…N1 and nO9-H11…O4 that represent the strong hydrogen bond and the
58
59 remaining weak hydrogen bonds are observed with the green colour regions at the respective
60
61
62 21
63
64
65
 1
2
3
4 regions. Stacking and the steric interactions are energyrepresented by green mixed brownish
5
6 and red color isosurfaces.
7
8
9
10
11
12
13
14
15
16
17 Gr_GC
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36 Gr_AT
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53 Gr_CAF-C
54
55
56
57
58
59
60
61
62 22
63
64
65
 1
2
3
4
5
6
7 Gr_CAF-T
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26 SiGr_GC
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45 SiGr_AT
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62 23
63
64
65
 1
2
3
4
5
6
7
SiGr_CAF-C
8
9
10
11
12
13
14
15
16
17
18
19 `
20
21
22
23
24
25
SiGr_CAF-T
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
SiGr-COOH_GC
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62 24
63
64
65
 1
2
3
4
SiGr-COOH_AT
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23 SiGr-COOH_CAF-C
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40 SiGr-COOH_CAF-T
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
Fig. 3 RDG (s) and sign (λ2)ρ along with the NCI isosurfaces for the DNA adsorbed
57
58
59 graphene models
60
61
62 25
63
64
65
 1
2
3
4 The strong hydrogen bonds N1-H1…N3, N3-H3…N1 and O9-H11…O4 as well as
5
6 O17-H29…O6 are observed with the blue regions in the corresponding complexes
7
8 SiGr-COOH_GC, SiGr-COOH_AT and SiGr-COOH_CAF-T respectively and all the
9
10 remaining weak bonds are witnessed by the green colour regions. Similarly, RDG map values
11
12 for the DNA adsorbed SiGr-COOH complexes range from -0.009 to -0.045, -0.008 to -0.046
13
14
a.u, -0.006 to -0.036 and -0.005 to -0.020 a.u for the respective complexes SiGr-COOH_AT,
15 SiGr-COOH_GC, SiGr-COOH_CAF-T and SiGr-COOH_CAF-C. The nature of the bonds in
16
17 those complexes was thus confirmed with the RDG analysis. These results confirm that DNA
18
19 base pairs are adsorbed with the graphene models via hydrogen bonds, Si-O(N) and stacking
20
21 interactions.
22
23
24
25 3.4 Natural bonding orbital analysis
26
27 NBO analysis is carried out to evaluate the orbital interaction energies, donor-
28
29 acceptor interactions and strength of interactions using the Fock matrix’s second-order
30
31 perturbation theory approach (Reed et al. 1988). In addition to the stabilisation energies
32
33 between the occupied lone pair NBOs N(Y) and unoccupied anti-bonding NBOs σ* (X-H),
34
35
NBO occupation numbers have been reported for the lone pairs N(Y) and anti-bonds σ* (X-H)
36 are listed in Table 1 which are calculated by using M06-2X/cc-pVDZ (Mudedla et al. 2014).
37
38 Hydrogen bond length has been contracted and elongated during the complex formation that
39
40 results from the charge transfer between them. The results show that in the case of the DNA
41
42 adsorbed pristine graphene model, the charge transfer between DNA base pairs and pristine
43
44 graphene is negligible, whereas in the case of DNA adsorbed SiGr and SiGr-COOH models,
45
46
considerable charge transfer has been noted. In addition, it is observed that high stabilisation
47 energies are found between the unoccupied orbital of Si and the lone pair of N(O).
48
49 The stabilisation energies lie between 0.4 and 30.8 kcal/mol, 0.5 and 32.0 kcal/mol, as
50
51 well as 0.1 and 34.5 kcal/mol for the DNA adsorbed pristine graphene, SiGr and SiGr-COOH
52
53 models, respectively. The stabilisation energy values are found between 19.9 and 34.5 kcal/mol,
54
55 1.4 to 19.4 kcal/mol, 3.0 and 13.6 kcal/mol, 4.4 and 4.6 kcal/mol, as well as 0.1 and 1.5
56
kcal/mol respectively for the corresponding bonds N-H...N, N-H...O, O-H...O, C-H...N and C-
57
58 H...O. Thus the higher adsorption energies arise due to highly stabilised strong bonds N-H...N,
59
60 N-H...O, O-H...O. Though C-H...N and C-H...O have least stabilisation energies, those were
61
62 26
63
64
65
 1
2
3
4 estimated due to strong influence in the DNA, and the stabilisation energy order is obtained as
5
6 below:
7
8 N-H...N > N-H...O > O-H...O > C-H...N > C-H...O
9
10 In the case of DNA adsorbed SiGr-COOH models, while comparing the N-H…N bonds,
11
12 anti-bonding donor bond lengthening (red shift) is observed in the N1-H1…N3 bond with the
13
14
corresponding hydrogen bond length of 1.765 Å in the complex SiGr-COOH_GC. Thus, the
15 short hydrogen bond lengths result in the electron density transfer to the anti-bonding donor
16
17 N1-H1 from the lone pair N3, leading to the highest stabilisation energy of 34.5 kcal/mol. The
18
19 occupancy values of the anti-bonding donor in the proton donor σ* (X-H) and the lone pair of
20
21 the proton acceptor were found to be 0.086 and 1.850 a.u which is lesser than the corresponding
22
23 monomer values of 0.059 and 1.870 a.u respectively with the difference of 0.027 and 0.020 a.u.
24
25
This caused the N1-H1 bond to elongate by 0.015 Å and weaken due to the charge transfer of
26 0.027 e from the lone pair N3 to the anti-bonding donor N1-H1. Thus in the N-H…N bonds,
27
28 high stabilisation energies of 32.0, 31.8, 30.8, 28.3 and 19.9 kcal/mol are observed for the
29
30 complexes SiGr_AT, SiGr-COOH_AT, Gr_AT and SiGr_GC. Donor covalent bond
31
32 lengthening and contraction occur due to the charge transfer between the lone pair of the
33
34 protein acceptor and antibonding donor in the proton donor. In addition, bond length elongation
35
and contraction occur in the donor covalent bonds of N-H bond ranges between 0.003 and
36
37 0.703 Å with the corresponding hydrogen bond length of 1.811, 1.768, 1.756, 1.761 and 1.875
38
39 Å. These strong hydrogen bonds with the short hydrogen bond lengths transfer the electron
40
41 density from the lone pairs N(N1, N1, N1, N3 and N3) to the antibonding donors N-H (N3-H3,
42
43 N3-H3, N3-H3, N1-H1 and N1-H1). The corresponding occupancy values of anti-bonding
44
45 donors and lone pairs are found to be 0.080, 0.079, 0.059, 0.067 and 0.060 a.u as well as 1.866,
46 1.847, 1.860, 1.850 and 1.865 a.u with the corresponding charge transfer values of 0.005, 0.006,
47
48 0.026, 0.008 and 0.001 e respectively. Generally, while considering N-H…N hydrogen bonds,
49
50 elongation in the anti-bonding donors tends to give high stabilisation energies, while in the
51
52 present work, higher stabilisation energy with the contraction in the anti-bonding donors has
53
54 been observed because while attempting the stabilisation, the hydrogen atom would face the
55
56 short-range repulsive forces.
57 In the case of N-H…O hydrogen bonds, higher stabilisation energy values of 19.4, 16.6
58
59 and 13.2 kcal/mol are obtained for Gr_GC, Gr_CAF-T & SiGr_GC complexes, respectively,
60
61
62 27
63
64
65
 1
2
3
4 with the donor bond elongation and contraction ranges between o and 2.041 Å. While
5
6 comparing the N-H…O bonds, N4-H4a…O6 (Gr_GC) has the highest stabilisation energy of
7
8 19.4 kcal/mol with a short hydrogen bond length of 1.755 Å. In the bond N4-H4a…O6, a high
9
10 charge transfer of 0.004 e from the lone pair O6 to the anti-bonding donor N4-H4a with the
11
12 bond contraction of 0.002 Å occurs. In addition, O-H…O hydrogen bonds are observed in DNA
13
14
adsorbed SiGr-COOH model, which is also responsible for the strong adsorption energies in
15 those complexes. Especially in the bonds O17-H29…O6 (SiGr-COOH_CAF-T) and O9-
16
17 H11…O4 (SiGr-COOH_AT), higher stabilisation energies of 13.6 and 10.3 kcal/mol with the
18
19 donor bond elongation in the donor bond O17-H29 (0.017 Å) and O9-H11 (0.019 Å) could be
20
21 observed. Shorter hydrogen bonds have been observed in the bonds O17-H29…O6 (1.736 Å)
22
23 and O9-H11…O4 (1.798 Å) with the occupation values of 1.950 and 1.946 a.u for the lone
24
25
pairs O6 as well as O4 and 0.048 and 0.045 a.u in the anti-bonding donors O17-H29 and O9-
26 H11 respectively which results in the charge transfer values of 0.036 and 0.037 e.
27
28 In the C-H…N bonds, C1-H1a…N3 and C1-H1a…N3 are observed with the
29
30 corresponding stabilisation energies of 4.6 and 4.4 kcal/mol with the charge transfer of 0.001e
31
32 with the corresponding hydrogen bond lengths of 2.282 and 2.316 Å. Thus, hydrogen bond
33
34 length is directly proportional to the stabilisation energies resulting from the charge transfer
35
from the lone pair to its corresponding anti-bonding donors. While comparing the C-H…N
36
37 bonds, stabilisation energies are between 1.0 and 1.5 kcal/mol with negligible charge transfer.
38
39 The strength of the hydrogen bonds is measured by the stabilisation energy of the respective
40
41 hydrogen bond values, and it is not a sign of overall structural stability (Hobza and Sponer
42
43 1999).
44
45 In the Si-N(O) interaction, high stabilisation energies are obtained between the
46 unoccupied orbital of Si and the lone pair of O (N) in the range of 81.1 to 187.7 kcal/mol and
47
48 are given in Table 1. In the complex SiGr-COOH_AT, the highest stabilisation energies of
49
50 187.7 kcal/mol are observed, followed by SiGr-COOH_GC (140.3 kcal/mol), SiGr-
51
52 COOH_CAF-T (138.1 kcal/mol) and SiGr-COOH_CAF-T (127.4 kcal/mol). While in the
53
54 complexes SiGr_GC and SiGr_CAF-T, stabilisation energies have been obtained as 126.9 and
55
56 81.1 kcal/mol. This reveals that high adsorption energies of all the complexes arise due to
57 hydrogen bond interactions, π-π stacking interactions and Si-O(N) interactions.
58
59
60
61
62 28
63
64
65
 1
2
3
4 In this study, charge transfer and structural changes (bond contraction and elongation) in
5
6 the hydrogen bonds have been analysed to examine the reason for donor covalent bond
7
8 expansions and contractions. From the results, it is obvious that the doping of Si and COOH
9
10 functionalisation into the graphene could enhance the chemical reactivity of the graphene
11
12 towards the DNA base pairs. Hence from the results perceived, it is observed that strong bonds
13
14
occur in the DNA interacted SiGr-COOH molecules with the high delocalisation charge values
15 that form the most stable structure, which could be used in biosensing applications.
16
17
18
19 3.5 Atoms in molecules (AIM) analysis
20
21 AIM analysis is used to investigate the nature of bonding between the atoms in terms of
22
23 electron density (ρ), bond ellipticity (ε) and the Laplacian of the electron density (𝛁²ρ) at the
24
25
Bond critical points (BCP) (Bader 1985). Bond strength and bond type are observed from the
26 values of electron density (ρ) and the Laplacian of the electron density at BCP (Iogansen 1999).
27
28 The nature of the bonds is derived through the sign of the 𝛁²ρ, in which the negative sign of 𝛁²ρ
29
30 represents the formation of covalent bond. On the other hand, positive sign of 𝛁²ρ represents
31
32 the closed shell interaction such as hydrogen bond, ionic and π-π stacking interactions.
33
34 Topological parameters for the hydrogen bonds, N-H…N, N-H…O, O-H…O, C-H…N & C-
35
36 H…O and for the covalent bonds Si-O and Si-N have been presented in Table 3. From the
37 results, it is observed that positive values of 𝛁²ρ at BCP in the DNA adsorbed graphene models
38
39 represent the hydrogen bond and π-π stacking interactions. Popelier criteria values of the ρ and
40
41 𝛁²ρ are observed to be in the range of 0.002 to 0.34 a.u and 0.016 to 0.13 a.u, respectively, for
42
43 the hydrogen bond interactions (Popelier and Bader 1992),(Koch and Popelier 1995). In this
44
45 study, ρ and 𝛁²ρ values are in the range of 0.006 to 0.067 a.u. and 0.021 to 0.154 a.u.
46
47 respectively for the hydrogen bond interactions. While considering topological parameters of
48
49
hydrogen bonds in DNA adsorbed graphene models, SiGr-COOH models have the highest
50 values of 0.006 to 0.081 a.u and 0.022 to 0.139 a.u for the corresponding ρ and 𝛁²ρ parameters.
51
52 In addition, DNA adsorbed SiGr and pristine graphene complexes are observed with the values
53
54 of 0.008 to 0.067 a.u & 0.028 to 0.154 a.u and 0.006 to 0.047 a.u & 0.021 to 0.124 a.u for the
55
56 corresponding parameters ρ and 𝛁²ρ respectively.
57
58
59
60
61
62 29
63
64
65
 1
2
3
4 Table 3 Topological parameters of the DNA base pair adsorbed graphene models.
5
6
7
8
9 Bonding type ρ 𝛁² ρ in ε in V(r) G(r) H(r)
10 (a.u) (a.u) (a.u) (a.u) (a.u) (a.u)
11 Gr-AT
12 N10-H23…O7 0.028 0.089 0.037 -0.0217 0.0220 0.0003
13 N2-H25…N16 0.047 0.105 0.060 -0.0334 0.0299 -0.0036
14 C15-H22…O9 0.006 0.021 0.014 -0.0034 0.0043 0.0009
15
Gr_GC
16
17 N27-H28…O10 0.037 0.124 0.032 -0.0292 0.0300 0.0009
18 N11-H12…O17 0.029 0.094 0.050 -0.0227 0.0230 0.0004
19 N8-H14…N20 0.035 0.090 0.064 -0.0238 0.0232 -0.0007
20 Gr_CAF-C
21 N20-H21…O33 0.021 0.078 0.018 -0.0170 0.0183 0.0012
22 C26-H7…N13 0.015 0.044 0.065 -0.0097 0.0104 0.0007
23 Gr_CAF-T
24 N2-H19…O38 0.028 0.109 0.015 -0.0226 0.0250 0.0024
25 C28-H17…O7 0.012 0.040 0.044 -0.0089 0.0094 0.0006
26
27 SiGr_AT
28 N10-H23…O7 0.022 0.067 0.040 -0.0173 0.0170 -0.0003
29 N2-H25…N16 0.041 0.100 0.072 -0.0290 0.0270 -0.0020
30 C15-H22…O9 0.008 0.028 0.159 -0.0052 0.0062 0.0009
31 SiGr_GC
32 N27-H28…O10 0.027 0.085 0.036 -0.0212 0.0211 -0.0001
33 N8-H14…N20 0.046 0.104 0.060 -0.0330 0.0295 -0.0035
34 N11-H12…O17 0.067 0.154 0.037 -0.0610 0.0497 -0.0113
35 Si31-N11 0.074 0.200 0.027 -0.1071 0.0786 -0.0285
36
SiGr_CAF-C
37
N60-H69…O78 0.017 0.064 0.032 -0.0144 0.0152 0.0007
38
39 C74-H72…N59 0.016 0.047 0.055 -0.0106 0.0112 0.0006
40 SiGr_CAF-T
41 N70-H73…O74 0.041 0.146 0.005 -0.0331 0.0348 0.0016
42 Si2-O72 0.081 0.393 0.097 -0.1374 0.1178 -0.0196
43 SiGr-COOH_AT
44 N10-H23…O7 0.022 0.063 0.058 -0.0170 0.0164 -0.0007
45 N16-H25…N2 0.045 0.104 0.056 -0.0322 0.0292 -0.0030
46 C15-H22…O9 0.007 0.027 0.261 -0.0046 0.0057 0.0011
47 O99-H106…O7 0.032 0.107 0.023 -0.0246 0.0257 0.0011
48
N10-H24…O102 0.020 0.065 0.098 -0.0160 0.0161 0.0001
49
N17-H21…O105 0.020 0.064 0.042 -0.0160 0.0159 -0.0001
50
C18-H20…O104 0.010 0.037 0.404 -0.0070 0.0081 0.0011
51
52 Si33-O9 0.098 0.566 0.094 -0.1849 0.1632 -0.0217
53 SiGr-COOH_GC
54 N11-H12…O17 0.081 0.139 0.030 -0.0822 0.0584 -0.0238
55 N8-H14…N200 0.046 0.104 0.059 -0.0328 0.0294 -0.0033
56 N27-H28…O10 0.025 0.077 0.039 -0.0197 0.0195 -0.0002
57 N2-H15…O112 0.014 0.048 0.143 -0.0110 0.0115 0.0005
58 C1-H16…O100 0.008 0.032 0.835 -0.0052 0.0065 0.0013
59 N27-H29…O81 0.019 0.061 0.043 -0.0158 0.0155 -0.0003
60
61
62 30
63
64
65
 1
2
3
4 Si31-N11 0.082 0.258 0.012 -0.1279 0.0963 -0.0317
5
6 SiGr-COOH_CAF-C
7 C73-H74…O89 0.010 0.037 0.120 -0.0071 0.0081 0.0010
8 C77-H80…O87 0.006 0.022 0.071 -0.0038 0.0046 0.0009
9 C77-H78…O116 0.007 0.026 0.052 -0.0048 0.0057 0.0009
10 N52-H58…O99 0.010 0.034 0.101 -0.0072 0.0078 0.0006
11 N48-H50…O103 0.012 0.040 0.089 -0.0091 0.0096 0.0005
12 Si2-O65 0.093 0.522 0.050 -0.1708 0.1507 -0.2012
13
SiGr-COOH_CAF-T
14
N64-H67…O68 0.020 0.067 0.099 -0.0164 0.0165 0.0001
15
C70-H89…O66 0.012 0.053 1.629 -0.0098 0.0115 0.0016
16
17 O114-H116…O88 0.036 0.128 0.019 -0.0282 0.0301 0.0018
18 C84-H87…O106 0.008 0.029 0.354 -0.0052 0.0062 0.0010
19 O99-H100…O63 0.017 0.050 0.043 -0.0134 0.0129 -0.0005
20 O102-H103…O63 0.018 0.063 0.104 -0.0149 0.0153 0.0004
21 Si2-O66 0.085 0.440 0.143 -0.1489 0.1295 -0.0194
22
23
24 While comparing DNA adsorbed graphene models N11-H12…O17 bond in the complex
25
26 SiGr-COOH_GC is found to have the highest ρ and 𝛁²ρ values of 0.081 & 0.139 a.u with the
27
28 highest stabilisation energy of 30.2 kcal/mol with low hydrogen bond length (1.478) and high
29
30 ellipticity value of 0.030 a.u. In addition, the potential electron energy density V(rBCP), kinetic
31
32
electron energy density G(rBCP) and the total energy density HBCP are also obtained. The Si-
33 N(O) bonds are observed in the DNA adsorbed SiGr and DNA adsorbed SiGr-COOH models,
34
35 and the parameters ρ and 𝛁²ρ are found to be in the range of 0.074 to 0.098 a.u and 0.200 to
36
37 0.566 a.u respectively. While comparing the Si-N(O) bonds, the highest topological parameters
38
39 have been obtained for the bond Si33-O9 in the complex SiGr-COOH_AT with the
40
41 corresponding values of 0.098 a.u and 0.566 a.u. for the parameters ρ and 𝛁²ρ respectively.
42
43
Generally, the negative values of HBCP reflect the covalent nature, and the positive value
44 indicates the non-covalent nature (Senthilkumar et al. 2013). The positive values of the HBCP
45
46 indicate more delocalised electrons in the closed-shell interaction. Table 4 shows that Si-N(O)
47
48 bonds in all the silicon-doped graphene models are observed with positive 𝛁²ρ values as well as
49
50 negative HBCP values that indicate the partial electrostatic and covalent interactions. Thus, the
51
52 increased stability of SiGr and SiGr-COOH are due to the Si-N(O) bonds (partial electrostatic
53
54
and covalent interactions) along with the hydrogen bonds and π-π stacking interactions.
55
56
57
58
59
60
61
62 31
63
64
65
 1
2
3
4 Table 4 Occupation number of the Lone pair occupied orbital (LP), Unoccupied orbital
5
6 (LP*) and the hydrogen bond stabilisation energy E(2) of Si-N(O) interaction calculated at
7
8 M06-2X/cc-pVDZ level of theory
9
10
11
12 Complex Charge-transfer Occupation energy E(2)
13 interaction (a.u) (kcal/mol)
14
15 SiG_GC LP of N → LP* of Si 1.70131 0.42775 126.9
16 SiG_CAF-T LP of O → LP* of Si 1.66153 0.39429 81.1
17
18 SiG-COOH_AT LP of O → LP* of Si 1.69715 0.38405 187.7
19 SiG-COOH_GC LP of N → LP* of Si 1.68858 0.42231 140.4
20
21
22
23
3.6 Partial density of states and Frontier molecular orbital
24 The PDOS of graphene (Gr_AT, Gr_GC, Gr_CAF-C and CAF-T), Si-doped graphene
25
26 (SiGr_AT, SiGr_GC, SiGr_CAF-C and SiGr_CAF-T) and COOH-functionalised Si-doped
27
28 graphene (SiGr-COOH_AT, SiGr-COOH_GC, SiGr-COOH_CAF-C, and SiGr-COOH_CAF-
29
30 T) are plotted and shown in Fig. 4 to confirm the bonding mechanism further.
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47 Gr_AT SiGr_AT SiGr-COOH_AT
48
49
50
51
52
53
54
55
56
57
58
59
60 Gr_GC SiGr_GC SiGr-COOH_GC
61
62 32
63
64
65
 1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
Gr_CAF-C SiGr_CAF-C SiGr-COOH_ CAF-C
18
19
20
21
22
23
24
25
26
27
28
29
30 Gr_CAF-T SiGr_CAF-T SiGr-COOH_ CAF-T
31
32
33 Fig. 4 Partial Density of States of DNA adsorbed graphene models
34
35
36
37
38 In the PDOS plot, the black region corresponds to LUMO or conduction band, and the
39
40 green region corresponds to the HOMO or valence band region. In the case of Gr-AT base-pair
41
42 complexes, the conduction band spans from -1.83 to beyond 20.00 eV, and the valence band
43
44 spans from -5.85 to beyond -20.00 eV. The PDOS are distributed, most of which originate from
45
46 the electronic transitions from the occupied states localised on the Gr to the unoccupied states
47
localised on the base pairs. The corresponding energy gap is about 4.01 eV. The close
48
49 inspection of the complexes shows that the partial density distribution is similar for carbon and
50
51 nitrogen atoms in the SiGr_AT complex. The valence band and the conduction band regions
52
53 span from approximately -5.63 to beyond -20.00 eV and -1.88 to beyond 20.00 eV respectively.
54
55 The energy gap of the complex is found to be 3.75 eV. In the case of the SiGr-COOH_AT
56
57 complex, the valence band and conduction band span from -6.32 to beyond -20.00 eV and -3.07
58 to beyond 20.00 eV, respectively, with the band gap of 3.24 eV. From the obtained results it is
59
60 inferred that the homo region of silicon-doped and COOH-functionalised silicon-doped
61
62 33
63
64
65
 1
2
3
4 graphene with the base pairs shows high stability compared to the pristine graphene with base
5
6 pairs. While comparing carbon, hydrogen and oxygen atoms, silicon has major occupancy,
7
8 expanding the majority in the conduction band in the range of 4 to 20 eV.
9
10 In the Gr_CAF-C complex, it is observed that the oxygen atom has several peaks similar
11
12 to the carbon atom, and the hydrogen atom has the least number of peaks that contribute less to
13
14
the corresponding complex with an energy gap of 3.99 eV. The valence and conduction bands
15 are in the range of -5.88 to beyond -20.00 eV and -1.89 to beyond 20.00 eV, respectively.
16
17 SiGr_CAF-C shows the majority contributions of nitrogen and silicon atoms, and the energy
18
19 gap is about 3.73 eV. The conduction band spans from -1.76 to beyond 20.00 eV, and the
20
21 valence band spans from -5.49 to beyond -20.00 eV. The PDOS plot for the complex SiGr-
22
23 COOH_CAF-C shows a valence band and conduction band spanning from -5.93 to above
24
25
-20.00 eV and -2.74 to 20.00 eV with the corresponding energy gap of 3.18 eV. The electrons
26 of each graphene atom are highly localised, and the orbital contribution for this state is
27
28 enhanced by 3d orbital of Si atom and oxygen atom. In addition, Si atoms induce their
29
30 electronic states deep inside the conduction and valence bands of the complexes SiGr_CAF-C
31
32 and SiGr-COOH_CAF-C. The band gap differences indicate a significant effect of
33
34 intramolecular charge transfer, where the backbone nitrogen atom localises the electron and
35
breaks the symmetry of the structure.
36
37 However, a closer inspection of the plot reveals that the band gap’s extent greatly
38
39 depends on the nature of the doping agents. In the Gr_CAF-T complex, it has been found that
40
41 the carbon and nitrogen atoms have a similar peak in the range of -20 to 20 eV, and the
42
43 corresponding energy gap is 4.01 eV. Besides, the conduction band spans from -1.80 to beyond
44
45 20.00 eV, and the valence band spans from -5.81 eV to beyond -20.00 eV. In the complex
46 SiGr_CAF-T, Si contributes to the PDOS plot at -20 to 20 eV. In addition, the oxygen atom
47
48 spans the region between 6 and 20 eV and beyond, and the energy gap of the system is 3.27 eV.
49
50 In addition, conduction and valence bands are observed in the range of -2.93 to beyond 20.00
51
52 eV and -6.38 to beyond -20.00 eV, respectively, for the complex SiGr-COOH_CAF-T.
53
54 In the case of the Gr_GC complex, the nitrogen and carbon atoms show a major
55
56 contribution in the PDOS plot with the corresponding energy gap of 3.98 eV. For the PDOS of
57 SiGr_GC and SiGr-COOH_GC complexes, silicon shows the major contribution with the
58
59 energy gap values of 3.68 eV and 3.31 eV, respectively. The conduction and valence band
60
61
62 34
63
64
65
 1
2
3
4 values are observed in the range of -5.82 to beyond -20.00 eV & -1.84 to beyond 20.00 eV
5
6 (Gr_GC), -5.08 to beyond -20.00 eV & -1.40 to beyond 20.00 eV (SiGr_GC) and -6.14 to
7
8 beyond -20.00 eV & -2.82 to beyond 20.00 eV (SiGr-COOH_GC).Thus while comparing the
9
10 complexes, the significant variations in the HOMO–LUMO gap and PDOS plot, DNA base
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12 pairs interact with Si-doped graphene, and COOH-functionalised Si-doped graphene can be
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exploited for possible applications in the sensing of DNA nucleobases.
15 The molecular orbital analysis of the DNA base pair interacting with graphene is shown
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17 in Fig. 5. The charge transfer between the base pairs and Si-doped Graphene as well as COOH
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19 functionalised Si-doped graphene is comparatively higher than the pristine graphene. In the
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21 case of base pair interacted Si-doped graphene, both HOMO and LUMO are localised on Si-
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23 doped graphene as well as on the base pairs. The HOMO of the base pair interacted graphene
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complexes is localised over the graphene and LUMO is distributed over the base pairs. It can be
26 seen that both HOMO and LUMO of SiGr have major contribution from Si atom. The
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28 electrophilic nature of Si is higher than nucleophilic nature that results the strong interaction
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30 between Si and O(N).The decreased HOMO–LUMO gap leads to the increased number of
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32 electrons in the conduction band and thus enhances the conductivity. Thus variations lead to the
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34 change in the conductivity of Si-doped graphene and COOH functionalised Si-doped graphene
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compared to pristine graphene. These results are useful for the development of new sensors.
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55 Fig. 5 The molecular orbital analysis diagram of the DNA base pair interacting
56 graphene complexes (i) Top view (ii) Side view
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5 3.7 UV-visible absorption spectra
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The UV-vis spectrum is calculated for the isolated DNA base pairs and graphene
8 models, as well as DNA, adsorbed graphene models, to observe the stability and the binding
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10 mode of DNA with graphene models by using time-dependent density functional theory (TD-
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12 DFT) with M06-2X/6-31+G** and are shown in Fig. 6. From the figure, it is observed that
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14 during the adsorption of DNA with graphene models, the absorption spectrum of the DNA base
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16 pairs and graphene models are shifted based on their interaction strength (Han et al. 2019; Bhatt
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et al. 2016). Considering the absorption spectrum of isolated DNA base pairs, peaks are
19 observed at the wavelength range of 195 to 258 nm. In the case of the GC base pair, peaks have
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21 been observed at the wavelength values of 213, 224, 237 and 258 nm with the corresponding
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23 oscillator strength (f) values of 0.14, 0.44, 0.17 and 0.02 a.u. In addition, peaks have been
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25 witnessed at the wavelength values of 209, 230 & 235 nm (AT), 199, 213 & 249 nm (CAF-C)
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27 and 195, 233 & 243 nm (CAF-T) with the corresponding oscillator strength values of 0.02, 0.29
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& 0.26 (AT), 0.04, 0.13 & 0.28 a.u (CAF-C) and 0.08, 0.20 & 0.17 a.u. (CAF-T). All the
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30 observed values agree with the experimental DNA absorption values of 260 nm (Wolfe et al.
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32 2002; Labarca and Paigen 1980). During the adsorption of DNA with graphene models, the
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34 absorption spectrum is red-shifted (bathochromic).
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36 In the isolated SiGr-COOH graphene model, six peaks are observed in the absorption
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38 spectrum at the wavelength of 318, 334, 356, 377, 411 & 521 nm with the corresponding
39 oscillator strength (f) values of 0.25, 0.14, 0.07, 0.59, 0.06 & 0.42 a.u. During the adsorption of
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41 AT base pairs with SiGr-COOH, peaks are shifted into 335, 362, 391, 405, 547 & 655 nm with
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43 the corresponding oscillator strength values of 0.06, 0.14, 0.19, 0.06, 0.10 & 0.25 a.u.
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45 COOH_GC), 316, 351, 371, 398, 464 & 513 nm (SiGr-COOH_CAF-C) and 358, 377, 402, 511,
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47 550 & 697 (SiGr-COOH_CAF-T) nm with the corresponding oscillator strength values of 0.07,
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0.13, 0.21, 0.01, 0.09 & 0.26 a.u (SiGr-COOH_GC), 0.14, 0.11, 0.36, 0.03, 0.03 & 0.28 a.u
50 (SiGr-COOH_CAF-C) and 0.11, 0.09, 0.04, 0.08, 0.25 & 0.07 a.u (SiGr-COOH_CAF-T). The
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52 absorption spectrum of isolated SiGr base pair exhibits bands at 312, 326, 350, 375, 405 & 515
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54 nm with the oscillator strength values of 0.16, 0.26, 0.06, 0.38, 0.11 & 0.29 a.u respectively.
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41 The absorption spectrum is red shifte
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59 Fig. 6 UV-Vis absorption spectrum of DNA with graphene models
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4 In the case of SiGr_GC complex, the spectrum is redshifted to the values of 334 nm
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6 (f=0.03a.u), 350 nm (f=0.06 a.u), 363 nm (f=0.16 a.u), 420 nm (f=0.01a.u) 507 nm (f=0.09 a.u)
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8 and 534 nm (f=0.25 a.u). In addition, the peaks shifted to 310, 339, 367, 403, 459 & 509 nm
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10 (SiGr_AT), 315, 351, 370, 400, 464 & 513 nm (SiGr_CAF-C) and 357, 378, 401, 511, 551 &
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12 698 (SiGr_CAF-T) nm with the corresponding oscillator strength values of 0.37, 0.03, 0.40,
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0.04, 0.02 & 0.31 a.u (SiGr_AT), 0.14, 0.11, 0.37, 0.03, 0.03 & 0.28 a.u (SiGr_CAF-C) and
15 0.11, 0.10, 0.03, 0.08, 0.24 & 0.08 a.u (SiGr_CAF-T), respectively. Some values are found to
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17 be lesser than the monomer values that are attributed to hypochromism where coupling π orbital
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19 is partially filled by electrons that decrease the transition probabilities. The absorption spectrum
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21 with the values of 291, 302, 337 and 442 nm were observed with the oscillatory strength values
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23 of 0.58, 0.71, 0.90 and 0.49 a.u respectively for the isolated graphene model and for the Gr_GC
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the increased values are observed at the wavelengths of 294, 307, 342 and 456 with the
26 oscillator strength values of 0.22, 0.64, 0.46 and 0.0.39 respectively. While in the remaining
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28 DNA adsorbed graphene models, the absorption spectrum exhibits bands at 295, 307, 341 &
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30 449 nm (Gr_AT), 292, 308, 347 & 452 nm (Gr_CAF-C) and 292, 308, 347 & 452 nm
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32 (Gr_CAF-T) with the oscillator strength values of 0.29, 0.62, 0.57 & 0.46 a.u (Gr_AT), 0.20,
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34 0.66, 0.58 & 0.43 a.u (Gr_CAF-C) and 0.52, 0.46, 0.76 & 0.41 respectively. Thus, in consistent
35
with the strength of the adsorption of DNA with the graphene models, significant changes of
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37 hypochromism and bathochromism are observed that confirms the strong intercalation binding
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39 involving hydrogen and stacking interactions.
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41
42
43 4 Conclusion
44
45 This investigation reports the adsorption of DNA base pairs on the surface of pristine
46 graphene (Gr), silicon-doped graphene (SiGr) and COOH-functionalised Si-doped graphene (SiGr-
47
48 COOH) and changes in the electronic structure are studied by DFT methods.
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50 DNA normal and modified base pairs adsorbed on SiGr-COOH have been observed for
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52 the first time using the theoretical methods, and the results may call for further experimental
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54 studies. DNA base pairs are strongly physisorbed on the graphene models due to the hydrogen
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56 bond, π-π stacking interactions and Si-O(N) interactions.
57 Among the DNA adsorbed graphene models, the DNA base pairs adsorbed SiGr-COOH
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59 model is found to have the highest adsorption energy of -202.83 kcal/mol, followed by the SiGr
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4 model, which would be highly beneficial in the biosensing field. In addition, among the various
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6 models, DNA base pairs adsorbed SiGr-COOH have high structural deformations with high
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8 adsorption energies. Especially in the bond N3-H3…N1, the highest contraction of 0.703 Å is
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10 observed in the proton donor N3-H3 with the angle deviation of 6.7º compared with the isolated
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12 DNA base pairs in the complex SiGr-COOH_AT with the high adsorption energy of -202.8
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kcal/mol. The occupancy of proton donor N3-H3 is found to have 0.079 a.u, which is decreased by
15 0.006 a.u than its isolated DNA base-pair value (0.085 a.u). Thus, the high charge transfer in the
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17 bonds leads to the strong adsorption energy in that complex resulting in high structural deviations.
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19 Thus among the various models, DNA base pairs adsorbed SiGr-COOH have high
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21 structural deformation, specifically in the active sites of carbonyl, amine and amide groups. These
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23 structural deviations stabilise the corresponding complexes leading to better adsorption energy
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25
between DNA base pairs and graphene models. Charge transfer and structural changes (bond
26 contraction and elongation) in the hydrogen bonds have been discussed to determine the reason for
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28 donor covalent bond expansions and contractions. The NBO analysis indicates that the charge
29
30 transfer between Si-doped graphene and COOH-functionalised Si-doped graphene with the base
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32 pairs is comparatively higher than pristine graphene. The stabilisation energies lie between 0.4 and
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34 30.8 kcal/mol, 0.5 and 32.0 kcal/mol and 0.1 and 34.5 kcal/mol for the DNA adsorbed pristine
35
graphene, SiGr and SiGr-COOH models. In addition, the reduced density gradient map and the NCI
36
37 isosurfaces are plotted to observe the bonds in those complexes.
38
39 AIM analysis reveals that increased electron density and Laplacian of electron
40
41 density values indicate a strong interaction. The positive values of the total electron density
42
43 H show the closed-shell interaction nature. HOMO and LUMO plots reveal the change in the
44
45 conductivity of Si-doped graphene and COOH-functionalised Si-doped graphene compared to
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47 pristine graphene. According to the PDOS plots, silicon’s contribution is high in silicon-doped
48
49
graphene and COOH-functionalised Si-doped graphene. In the DNA adsorbed graphene models,
50 significant changes in hypochromism and bathochromism confirms the strong intercalation binding
51
52 involving hydrogen and stacking interactions. These electronic structures and properties
53
54 observations are useful in new sensor development employing silicon-doped graphene and COOH-
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56 terminated Si-doped graphene. Overall, the findings from this study affirm that Si-doped graphene
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58 and the COOH-functionalised Si-doped graphene can act as a nucleobase pairs detection sensors.
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4 Conflicts of interest
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6 There are no conflicts to declare.
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8
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