Skip to main content
SpringerLink
Log in

2D silicene nanosheets for the detection of DNA nucleobases for genetic biomarker: a DFT study

  • Research
  • Published:
Structural Chemistry Aims and scope Submit manuscript

Abstract

The emerging hexagonal buckled 2D silicene holds promising electronic properties for new applications in the field of nanoelectronics. In this study, we have investigated the adsorption of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) on silicene surface. The binding affinity of studied nucleobases on silicene surface at M062X/6-31G* level of theory showed the following trend: C > G > T > A, which is in good agreement with previous results. The nucleobases are physisorbed on the silicene surface as observed with the non-covalent interactions (NCI) analysis; however, the atoms in molecule (AIM) analysis suggest that such bases have slight covalency while interacting with the surface. The semi-metallic behavior in silicene-nucleobases complexes was analyzed from total density of states (TDOS) and partial density of states (PDOS) plots. The spectral properties of nucleobases adsorbed on silicene surface can be monitored using infrared and Raman vibrational frequencies. The IR and Raman spectral studies showed to distinguish the adsorption of cytosine and adenine with larger shifts in the former case (63 cm−1) compared to the later one (14 cm−1). Such variations in the IR and Raman vibrational frequencies can be exploited for the monitoring and detection of nucleic acid biomarkers adsorbed on 2D silicene surface.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

Some data obtained through this work is provided in the supplementary information file.

References

  1. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171:737–738. https://doi.org/10.1038/171737a0

    Article  PubMed  CAS  Google Scholar 

  2. Klein D (2002) Quantification using real-time PCR technology: Applications and limitations. Trends Mol Med 8:257–260. https://doi.org/10.1016/S1471-4914(02)02355-9

    Article  PubMed  CAS  Google Scholar 

  3. Bustin SA (2000) Absolute quantification of mrna using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25:169–193. https://doi.org/10.1677/jme.0.0250169

    Article  PubMed  CAS  Google Scholar 

  4. Joshi H, Shirude PS, Bansal V et al (2004) Isothermal titration calorimetry studies on the binding of amino acids to gold nanoparticles. J Phys Chem B 108:11535–11540. https://doi.org/10.1021/jp048766z

    Article  CAS  Google Scholar 

  5. Shtogun YV, Woods LM, Dovbeshko GI (2007) Adsorption of adenine and thymine and their radicals on single-wall carbon nanotubes. J Phys Chem C 111:18174–18181. https://doi.org/10.1021/jp074270g

    Article  CAS  Google Scholar 

  6. Sheng M, Maragakis P, Papaloukas C, Kaxiras E (2007) DNA nucleoside interaction and identification with carbon nanotubes. Nano Lett 7:45–50. https://doi.org/10.1021/nl0619103

    Article  CAS  Google Scholar 

  7. Das A, Sood AK, Maiti PK et al (2008) Binding of nucleobases with single-walled carbon nanotubes: Theory and experiment. Chem Phys Lett 453:266–273. https://doi.org/10.1016/j.cplett.2008.01.057

    Article  CAS  Google Scholar 

  8. Yang H, Xia Y (2007) Bionanotechnology: Enabling biomedical research with nanomaterials. Adv Mater 19:3085–3087. https://doi.org/10.1002/adma.200702050

    Article  CAS  Google Scholar 

  9. Katz E, Willner I (2004) Integrated nanoparticle-biomolecule hybrid systems: Synthesis, properties, and applications. Angew Chemie - Int Ed 43:6042–6108. https://doi.org/10.1002/anie.200400651

    Article  CAS  Google Scholar 

  10. Li H, Huang J, Lv J et al (2005) Nanoparticle PCR: Nanogold-assisted PCR with enhanced specificity. Angew Chemie - Int Ed 117:5230–5233. https://doi.org/10.1002/ange.200500403

    Article  Google Scholar 

  11. Zhang J, Song S, Wang L et al (2007) A gold nanoparticle-based chronocoulometric dna sensor for amplified detection of dna. Nat Protoc 2:2888–2895. https://doi.org/10.1038/nprot.2007.419

    Article  PubMed  CAS  Google Scholar 

  12. Feldkamp U, Niemeyer CM (2006) Rational design of DNA nanoarchitectures. Angew Chemie - Int Ed 45:1856–1876. https://doi.org/10.1002/anie.200502358

    Article  CAS  Google Scholar 

  13. Barone PW, Baik S, Heller DA, Strano MS (2005) Near-infrared optical sensors based on single-walled carbon nanotubes. Nat Mater 4:86–92. https://doi.org/10.1038/nmat1276

    Article  PubMed  CAS  Google Scholar 

  14. Zhao X (2011) Self-assembly of DNA segments on graphene and carbon nanotube arrays in aqueous solution: A molecular simulation study. J Phys Chem C 115:6181–6189. https://doi.org/10.1021/jp110013r

    Article  CAS  Google Scholar 

  15. Paul A, Bhattacharya B (2010) DNA functionalized carbon nanotubes for nonbiological applications. Mater Manuf Process 25:891–908. https://doi.org/10.1080/10426911003720755

    Article  CAS  Google Scholar 

  16. Liu Z, Yang K, Lee ST (2011) Single-walled carbon nanotubes in biomedical imaging. J Mater Chem 21:586–598. https://doi.org/10.1039/c0jm02020f

    Article  CAS  Google Scholar 

  17. Yarotski DA, Kilina SV, Talin AA et al (2009) Scanning tunneling microscopy of DNA-wrapped carbon nanotubes. Nano Lett 9:12–17. https://doi.org/10.1021/nl801455t

    Article  PubMed  CAS  Google Scholar 

  18. Prasongkit J, Grigoriev A, Pathak B et al (2011) Transverse conductance of DNA nucleotides in a graphene nanogap from first principles. Nano Lett 11:1941–1945. https://doi.org/10.1021/nl200147x

    Article  PubMed  CAS  Google Scholar 

  19. Umadevi D, Sastry GN (2011) Quantum mechanical study of physisorption of nucleobases on carbon materials: Graphene versus carbon nanotubes. J Phys Chem Lett 2:1572–1576. https://doi.org/10.1021/jz200705w

    Article  CAS  Google Scholar 

  20. Le D, Kara A, Schröder E et al (2012) Physisorption of nucleobases on graphene: A comparative van der Waals study. J Phys Condens Matter 24:424210. https://doi.org/10.1088/0953-8984/24/42/424210

  21. Lee JH, Choi YK, Kim HJ et al (2013) Physisorption of DNA nucleobases on h -BN and graphene: VdW-corrected DFT calculations. J Phys Chem C 117:13435–13441. https://doi.org/10.1021/jp402403f

    Article  CAS  Google Scholar 

  22. Vovusha H, Sanyal S, Sanyal B (2013) Interaction of nucleobases and aromatic amino acids with graphene oxide and graphene flakes. J Phys Chem Lett 4:3710–3718. https://doi.org/10.1021/jz401929h

    Article  CAS  Google Scholar 

  23. Ranganathan SV, Halvorsen K, Myers CA et al (2016) Complex thermodynamic behavior of single-stranded nucleic acid adsorption to graphene surfaces. Langmuir 32:6028–6034. https://doi.org/10.1021/acs.langmuir.6b00456

    Article  PubMed  CAS  Google Scholar 

  24. Da ZL, Yang F, Yao Y (2015) Possible electric-field-induced superconducting states in doped silicene. Sci Rep 5:8203. https://doi.org/10.1038/srep08203

    Article  CAS  Google Scholar 

  25. Cahangirov S, Topsakal M, Aktürk E et al (2009) Two- and one-dimensional honeycomb structures of silicon and germanium. Phys Rev Lett 102:236804. https://doi.org/10.1103/PhysRevLett.102.236804

  26. Guzmán-Verri GG, Lew Yan Voon LC (2007) Electronic structure of silicon-based nanostructures. Phys Rev B - Condens Matter Mater Phys 76:075131. https://doi.org/10.1103/PhysRevB.76.075131

  27. Tang Q, Zhou Z (2013) Graphene-analogous low-dimensional materials. Prog Mater Sci 58:1244–1315. https://doi.org/10.1016/j.pmatsci.2013.04.003

    Article  CAS  Google Scholar 

  28. Kaloni TP, Tahir M, Schwingenschlögl U (2013) Quasi free-standing silicene in a superlattice with hexagonal boron nitride. Sci Rep 3:3192. https://doi.org/10.1038/srep03192

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  29. Gao J, Zhao J (2012) Initial geometries, interaction mechanism and high stability of silicene on Ag(111) surface. Sci Rep 2:861. https://doi.org/10.1038/srep00861

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  30. Gürel HH, Özçelik VO, Ciraci S (2013) Effects of charging and perpendicular electric field on the properties of silicene and germanene. J Phys Condens Matter 25:305007. https://doi.org/10.1088/0953-8984/25/30/305007

  31. Bishnoi B, Ghosh B (2014) Spin transport in N-armchair-edge silicene nanoribbons. J Comput Electron 13:186–191. https://doi.org/10.1007/s10825-013-0498-z

    Article  CAS  Google Scholar 

  32. Lan TB, Xu Y, Tan H et al (2019) Quantum anomalous Hall effect with Landau levels in nonuniformly strained silicene. J Appl Phys 126:104303. https://doi.org/10.1063/1.5121189

  33. Novoselov KS, Geim AK, Morozov SV et al (2004) Electric field in atomically thin carbon films. Science (80-) 306:666–669. https://doi.org/10.1126/science.1102896

  34. Kara A, Enriquez H, Seitsonen AP et al (2012) A review on silicene - New candidate for electronics. Surf Sci Rep 67:1–18. https://doi.org/10.1016/j.surfrep.2011.10.001

    Article  CAS  Google Scholar 

  35. Feng B, Ding Z, Meng S et al (2012) Evidence of silicene in honeycomb structures of silicon on Ag(111). Nano Lett 12:3507–3511. https://doi.org/10.1021/nl301047g

    Article  PubMed  CAS  Google Scholar 

  36. Vogt P, De Padova P, Quaresima C et al (2012) Silicene: Compelling experimental evidence for graphenelike two-dimensional silicon. Phys Rev Lett 108:155501. https://doi.org/10.1103/PhysRevLett.108.155501

  37. Chen L, Liu CC, Feng B et al (2012) Evidence for Dirac fermions in a honeycomb lattice based on silicon. Phys Rev Lett 109:056804. https://doi.org/10.1103/PhysRevLett.109.056804

  38. Chen L, Li H, Feng B et al (2013) Spontaneous symmetry breaking and dynamic phase transition in monolayer silicene. Phys Rev Lett 110:085504. https://doi.org/10.1103/PhysRevLett.110.085504

  39. Meng L, Wang Y, Zhang L et al (2013) Buckled silicene formation on Ir(111). Nano Lett 13:685–690. https://doi.org/10.1021/nl304347w

    Article  PubMed  CAS  Google Scholar 

  40. Fleurence A, Friedlein R, Ozaki T et al (2012) Experimental evidence for epitaxial silicene on diboride thin films. Phys Rev Lett 108:245501. https://doi.org/10.1103/PhysRevLett.108.245501

  41. Osborn TH, Farajian AA (2014) Silicene nanoribbons as carbon monoxide nanosensors with molecular resolution. Nano Res 7:945–952. https://doi.org/10.1007/s12274-014-0454-7

    Article  CAS  Google Scholar 

  42. Huang S, Kang W, Yang L (2013) Electronic structure and quasiparticle bandgap of silicene structures. Appl Phys Lett 102:133106. https://doi.org/10.1063/1.4801309

  43. Zhao J, Liu H, Yu Z et al (2016) Rise of silicene: A competitive 2D material. Prog Mater Sci 83:24–151. https://doi.org/10.1016/j.pmatsci.2016.04.001

    Article  CAS  Google Scholar 

  44. Amorim RG, Scheicher RH (2015) Silicene as a new potential DNA sequencing device. Nanotechnology 26:154002. https://doi.org/10.1088/0957-4484/26/15/154002

  45. Prasongkit J, Amorim RG, Chakraborty S et al (2015) Highly sensitive and selective gas detection based on silicene. J Phys Chem C 119:16934–16940. https://doi.org/10.1021/acs.jpcc.5b03635

    Article  CAS  Google Scholar 

  46. Aghaei SM, Monshi MM, Calizo I (2016) A theoretical study of gas adsorption on silicene nanoribbons and its application in a highly sensitive molecule sensor. RSC Adv 6:94417–94428. https://doi.org/10.1039/c6ra21293j

    Article  CAS  Google Scholar 

  47. Tritsaris GA, Kaxiras E, Meng S, Wang E (2013) Adsorption and diffusion of lithium on layered silicon for Li-ion storage. Nano Lett 13:2258–2263. https://doi.org/10.1021/nl400830u

    Article  PubMed  CAS  Google Scholar 

  48. Hu W, Li Z, Yang J (2017) Water on silicene: A hydrogen bond-autocatalyzed physisorption–chemisorption–dissociation transition. Nano Res 10:2223–2233. https://doi.org/10.1007/s12274-016-1411-4

    Article  CAS  Google Scholar 

  49. Feng JW, Liu YJ, Wang HX et al (2014) Gas adsorption on silicene: A theoretical study. Comput Mater Sci 87:218–226. https://doi.org/10.1016/j.commatsci.2014.02.025

    Article  CAS  Google Scholar 

  50. Hussain T, Kaewmaraya T, Chakraborty S, Ahuja R (2016) Defect and substitution-induced silicene sensor to probe toxic gases. J Phys Chem C 120:25256–25262. https://doi.org/10.1021/acs.jpcc.6b08973

    Article  CAS  Google Scholar 

  51. Hussain T, Vovusha H, Kaewmaraya T et al (2018) Adsorption characteristics of DNA nucleobases, aromatic amino acids and heterocyclic molecules on silicene and germanene monolayers. Sensors Actuators, B Chem 255:2713–2720. https://doi.org/10.1016/j.snb.2017.09.083

    Article  CAS  Google Scholar 

  52. Alesheikh S, Shahtahmassebi N, Rezaee Roknabadi M, Pilevar Shahri R (2017) Interaction of nucleobases with silicene nanoribbon: A density functional approach. Comput Theor Chem 1103:32–37. https://doi.org/10.1016/j.comptc.2017.01.016

    Article  CAS  Google Scholar 

  53. Li Q, Liu H, Tian Y et al (2020) Methylation detection and DNA sequencing based on adsorption of nucleobases on silicene nanoribbon. J Phys Chem C 124:10823–10831. https://doi.org/10.1021/acs.jpcc.0c01734

    Article  CAS  Google Scholar 

  54. Chandiramouli R, Nagarajan V (2019) Silicene nanosheet device with nanopore to identify the nucleobases – A first-principles perspective. Chem Phys Lett 730:70–75. https://doi.org/10.1016/j.cplett.2019.05.038

    Article  CAS  Google Scholar 

  55. Hull MC, Cambrea LR, Hovis JS (2005) Infrared spectroscopy of fluid lipid bilayers. Anal Chem 77:6096–6099. https://doi.org/10.1021/ac050990c

    Article  PubMed  CAS  Google Scholar 

  56. Griffiths PR, De Haseth JA (2006) Fourier transform infrared spectrometry, 2nd edn. John Wiley & Sons Inc, Hoboken, NJ, USA

    Google Scholar 

  57. Rodrigo D, Limaj O, Janner D, et al (2015) Mid-infrared plasmonic biosensing with graphene. Science 349:165–168. https://doi.org/10.1126/science.aab2051

  58. Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: Two new functionals and systematic testing of four M06-class functionals and 12 other function. Theor Chem Acc 120:215–241. https://doi.org/10.1007/s00214-007-0310-x

    Article  CAS  Google Scholar 

  59. Boys SF, Bernardi F (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19:553–566. https://doi.org/10.1080/00268977000101561

    Article  CAS  Google Scholar 

  60. Murray JS, Paulsen K, Politzer P (1994) Molecular surface electrostatic potentials in the analysis of non-hydrogen-bonding noncovalent interactions. Proc Indian Acad Sci - Chem Sci 106:267–275. https://doi.org/10.1007/BF02840749

    Article  CAS  Google Scholar 

  61. Sjoberg P, Politzer P (1990) Use of the electrostatic potential at the molecular surface to interpret and predict nucleophilic processes. J Phys Chem 94:3959–3961. https://doi.org/10.1021/j100373a017

    Article  CAS  Google Scholar 

  62. Politzer P, Laurence PR, Jayasuriya K (1985) Molecular electrostatic potentials: An effective tool for the elucidation of biochemical phenomena. Environ Health Perspect 61:191–202. https://doi.org/10.1289/ehp.8561191

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  63. Sen KD, Politzer P (1989) Characteristic features of the electrostatic potentials of singly negative monoatomic ions. J Chem Phys 90:4370–4372. https://doi.org/10.1063/1.456622

    Article  CAS  Google Scholar 

  64. Murray JS, Politzer P (2011) The electrostatic potential: An overview. Wiley Interdiscip Rev Comput Mol Sci 1:153–163. https://doi.org/10.1002/wcms.19

    Article  CAS  Google Scholar 

  65. Frisch MJ, Trucks GW, Schlegel HB, MAR GES, Cheeseman JR, Scalmani G, Barone V, Mennucci B, GA Petersson H, Nakatsuji M, Caricato X, Li HP, Hratchian AF, Izmaylov J, Bloino G, Zheng J et al (2009) Gaussian 09 (revision B1). Gaussian, Inc, Wallingford, CT

  66. Johnson ER, Keinan S, Mori-Sánchez P et al (2010) Revealing noncovalent interactions. J Am Chem Soc 132:6498–6506. https://doi.org/10.1021/ja100936w

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  67. Lu T, Chen F (2012) Multiwfn: A multifunctional wavefunction analyzer. J Comput Chem 33:580–592. https://doi.org/10.1002/jcc.22885

    Article  PubMed  CAS  Google Scholar 

  68. Jose D, Datta A (2011) Structures and electronic properties of silicene clusters: A promising material for FET and hydrogen storage. Phys Chem Phys 13:7304–7311. https://doi.org/10.1039/c0cp02580a

    Article  CAS  Google Scholar 

  69. Bhai S, Ganguly B (2020) Probing the interaction of nucleobases and fluorophore-tagged nucleobases with graphene surface: Adsorption and fluorescence studies. ChemistrySelect 5:3191–3200. https://doi.org/10.1002/slct.201904442

    Article  CAS  Google Scholar 

  70. Gadre SR, Pundlik SS (1997) Complementary electrostatics for the study of DNA base-pair interactions. J Phys Chem B 101:3298–3303. https://doi.org/10.1021/jp9640641

    Article  CAS  Google Scholar 

  71. Umadevi D, Narahari Sastry G (2015) Graphane versus graphene: a computational investigation of the interaction of nucleobases, aminoacids, heterocycles, small molecules (CO2, H2O, NH3, CH4, H2), metal ions and onium ions. Phys Chem Phys 17:30260–30269. https://doi.org/10.1039/c5cp05094d

    Article  CAS  Google Scholar 

  72. Chandler D (2005) Interfaces and the driving force of hydrophobic assembly. Nature 437:640–647. https://doi.org/10.1038/nature04162

    Article  PubMed  CAS  Google Scholar 

  73. Panigrahi SK, Desiraju GR (2007) Strong and weak hydrogen bonds in the protein-ligand interface. Proteins Struct Funct Genet 67:128–141. https://doi.org/10.1002/prot.21253

    Article  PubMed  CAS  Google Scholar 

  74. Fenniri H, Mathivanan P, Vidale KL et al (2001) Helical rosette nanotubes: Design, self-assembly, and characterization. J Am Chem Soc 123:3854–3855. https://doi.org/10.1021/ja005886l

    Article  PubMed  CAS  Google Scholar 

  75. Fiedler S, Broecker J, Keller S (2010) Protein folding in membranes. Cell Mol Life Sci 67:1779–1798. https://doi.org/10.1007/s00018-010-0259-0

    Article  PubMed  CAS  Google Scholar 

  76. Cremer D, Kraka E (1984) Chemical bonds without bonding electron density — Does the difference electron-density analysis suffice for a description of the chemical bond? Angew Chemie - Int Ed 23:627–628. https://doi.org/10.1002/anie.198406271

    Article  Google Scholar 

  77. Espinosa E, Alkorta I, Elguero J, Molins E (2002) From weak to strong interactions: A comprehensive analysis of the topological and energetic properties of the electron density distribution involving X-H⋯F-Y systems. J Chem Phys 117:5529–5542. https://doi.org/10.1063/1.1501133

    Article  CAS  Google Scholar 

  78. Bolotsky A, Butler D, Dong C et al (2019) Two-dimensional materials in biosensing and healthcare: From in vitro diagnostics to optogenetics and beyond. ACS Nano 13:9781–9810. https://doi.org/10.1021/acsnano.9b03632

    Article  PubMed  CAS  Google Scholar 

  79. Chen H, Cheng Z, Zhou X et al (2022) Emergence of surface-enhanced Raman scattering probes in near-infrared windows for biosensing and bioimaging. Anal Chem 94:143–164. https://doi.org/10.1021/acs.analchem.1c03646

    Article  PubMed  CAS  Google Scholar 

  80. Benevides JM, Overman SA, Thomas GJ (2005) Raman, polarized Raman and ultraviolet resonance Raman spectroscopy of nucleic acids and their complexes. J Raman Spectrosc 36:279–299. https://doi.org/10.1002/jrs.1324

    Article  CAS  Google Scholar 

  81. Butler HJ, Ashton L, Bird B et al (2016) Using Raman spectroscopy to characterize biological materials. Nat Protoc 11:664–687. https://doi.org/10.1038/nprot.2016.036

    Article  PubMed  CAS  Google Scholar 

  82. Baker MJ, Trevisan J, Bassan P et al (2014) Using Fourier transform IR spectroscopy to analyze biological materials. Nat Protoc 9:1771–1791. https://doi.org/10.1038/nprot.2014.110

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  83. Brandt MS, Fuchs HD, Stutzmann M et al (1992) The origin of visible luminescencefrom “porous silicon”: A new interpretation. Solid State Commun 81:307–312. https://doi.org/10.1016/0038-1098(92)90815-Q

    Article  CAS  Google Scholar 

  84. Zamanzadeh-Hanebuth N, Brandt MS, Stutzmann M (1998) Vibrational properties of siloxene: Isotope substitution studies. J Non Cryst Solids 227–230:503–506. https://doi.org/10.1016/S0022-3093(98)00336-6

    Article  Google Scholar 

  85. Ryan BJ, Hanrahan MP, Wang Y et al (2020) Silicene, siloxene, or silicane? Revealing the structure and optical properties of silicon nanosheets derived from calcium disilicide. Chem Mater 32:795–804. https://doi.org/10.1021/acs.chemmater.9b04180

    Article  CAS  Google Scholar 

  86. Yamanaka S, Matsu-ura H, Ishikawa M (1996) New deintercalation reaction of calcium from calcium disilicide. Synthesis of layered polysilane. Mater Res Bull 31:307–316. https://doi.org/10.1016/0025-5408(95)00195-6

    Article  CAS  Google Scholar 

  87. Fuchs HD, Stutzmann M, Brandt MS et al (1993) Porous silicon and siloxene: Vibrational and structural properties. Phys Rev B 48:8172–8189. https://doi.org/10.1103/PhysRevB.48.8172

    Article  CAS  Google Scholar 

  88. Meng X, Sasaki K, Sano K et al (2017) Synthesis of crystalline Si-based nanosheets by extraction of Ca from CaSi2 in inositol hexakisphosphate solution. Jpn J Appl Phys 56:05DE02. https://doi.org/10.7567/JJAP.56.05DE02

  89. Colarusso P, Zhang KQ, Guo B, Bernath PF (1997) The infrared spectra of uracil, thymine, and adenine in the gas phase. Chem Phys Lett 269:39–48. https://doi.org/10.1016/S0009-2614(97)00245-5

    Article  CAS  Google Scholar 

  90. Beć KB, Grabska J, Czarnecki MA et al (2019) IR spectra of crystalline nucleobases: Combination of periodic harmonic calculations with anharmonic corrections based on finite models. J Phys Chem B 123:10001–10013. https://doi.org/10.1021/acs.jpcb.9b06285

    Article  PubMed  CAS  Google Scholar 

  91. Fuchs HD, Stutzmann M, Brandt MS et al (1992) Visible luminescence from porous silicon and siloxene. Phys Scr 1992:309–313. https://doi.org/10.1088/0031-8949/1992/T45/067

    Article  Google Scholar 

  92. Brodsky MH, Cardona M, Cuomo JJ (1977) Infrared and Raman spectra of the silicon-hydrogen bonds in amorphous silicon prepared by glow discharge and sputtering. Phys Rev B 16:3556–3571. https://doi.org/10.1103/PhysRevB.16.3556

    Article  CAS  Google Scholar 

  93. Shanmugasundaram M, Puranik M (2009) Computational prediction of vibrational spectra of normal and modified DNA nucleobases. J Raman Spectrosc 40:1726–1748. https://doi.org/10.1002/jrs.2533

    Article  CAS  Google Scholar 

Download references

Acknowledgements

S.B. is thankful to AcSIR Ghaziabad, Uttar Pradesh-201002, India, for Ph.D. registration. S.B. acknowledges CSIR-SRF (31/028(0279)/2020-EMR-I) for the financial support. CSIR-CSMCRI registration number is 229/2022. We thank the anonymous reviewer for suggestions and comments that have helped us to improve the paper.

Author information

Authors and Affiliations

  1. Computational and Simulation Unit (Analytical and Environment Science Division and Centralized Instrument Facility), CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar-364002, Gujarat, India

    Surjit Bhai & Bishwajit Ganguly

  2. Academy of Scientific and Innovative Research (AcSIR), Uttar Pradesh, Ghaziabad, 201002, India

    Surjit Bhai & Bishwajit Ganguly

Authors
  1. Surjit Bhai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bishwajit Ganguly
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Surjit Bhai carried out all the DFT calculations and drafted the manuscript. Bishwajit Ganguly has analyzed the results and reviewed the original draft of the manuscript. All the authors have read and approved the manuscript for submission.

Corresponding author

Correspondence to Bishwajit Ganguly.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 3969 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bhai, S., Ganguly, B. 2D silicene nanosheets for the detection of DNA nucleobases for genetic biomarker: a DFT study. Struct Chem 35, 25–37 (2024). https://doi.org/10.1007/s11224-023-02144-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11224-023-02144-w

Keywords

Search

Navigation