TY  - JOUR
AU  - Djurišić, Ivana
AU  - Dražić, Miloš
AU  - Tomović, Aleksandar
AU  - Jovanović, Vladimir P.
AU  - Žikić, Radomir
PY  - 2021
UR  - http://rimsi.imsi.bg.ac.rs/handle/123456789/1412
AB  - The requirement for controllable frontier orbital energy shift in single-molecule devices based on electronic (tunneling) transport yielded several rules for device design that lean on molecular level pinning to the electrochemical potential of nano-electrodes. We previously found that the pinning (designated as the strong pinning) was the consequence of the bias-induced molecular charge accumulation related to the hybridization of the highest occupied molecular orbital (HOMO) with one of the electrodes. However, in the wide bias range, only "partial" pinning (designated as the weak pinning) happens. In this work, we address the bias-induced shift of molecular orbitals in a weak pinning regime, where no hybridization or covalent bonds with electrodes exist. We found using density functional theory coupled with non-equilibrium Green's functions that the energy shift of frontier molecular orbitals of benzene and nicotine, placed between H-terminated (3, 3) CNTs, in weak pinning regime, is driven only by the electrostatic potential energy of an empty gap. For nicotine, whose HOMO and LUMO (lowest unoccupied molecular orbital) are located on different sides of the gap center, we show that the HOMO-LUMO energy gap changes with bias. We developed a theoretical model of a dielectric in a gap to depict this behavior. Application-wise, we expect that the weak pinning effect would be observable in novel single-molecule sensors based on electronic transport and molecular rectifying as long as the system exhibits a non-resonant behavior, and could serve for molecular gap tuning in single-molecule readout such as DNA, RNA and protein sequencing, or harmful single-molecule detection in gas phase.
PB  - Springer, Dordrecht
T2  - Journal of Nanoparticle Research
T1  - Electrostatically driven energy shift of molecular orbitals of benzene and nicotine in carbon nanotube gaps
IS  - 1
VL  - 23
DO  - 10.1007/s11051-021-05139-y
ER  - 

@article{
author = "Djurišić, Ivana and Dražić, Miloš and Tomović, Aleksandar and Jovanović, Vladimir P. and Žikić, Radomir",
year = "2021",
abstract = "The requirement for controllable frontier orbital energy shift in single-molecule devices based on electronic (tunneling) transport yielded several rules for device design that lean on molecular level pinning to the electrochemical potential of nano-electrodes. We previously found that the pinning (designated as the strong pinning) was the consequence of the bias-induced molecular charge accumulation related to the hybridization of the highest occupied molecular orbital (HOMO) with one of the electrodes. However, in the wide bias range, only "partial" pinning (designated as the weak pinning) happens. In this work, we address the bias-induced shift of molecular orbitals in a weak pinning regime, where no hybridization or covalent bonds with electrodes exist. We found using density functional theory coupled with non-equilibrium Green's functions that the energy shift of frontier molecular orbitals of benzene and nicotine, placed between H-terminated (3, 3) CNTs, in weak pinning regime, is driven only by the electrostatic potential energy of an empty gap. For nicotine, whose HOMO and LUMO (lowest unoccupied molecular orbital) are located on different sides of the gap center, we show that the HOMO-LUMO energy gap changes with bias. We developed a theoretical model of a dielectric in a gap to depict this behavior. Application-wise, we expect that the weak pinning effect would be observable in novel single-molecule sensors based on electronic transport and molecular rectifying as long as the system exhibits a non-resonant behavior, and could serve for molecular gap tuning in single-molecule readout such as DNA, RNA and protein sequencing, or harmful single-molecule detection in gas phase.",
publisher = "Springer, Dordrecht",
journal = "Journal of Nanoparticle Research",
title = "Electrostatically driven energy shift of molecular orbitals of benzene and nicotine in carbon nanotube gaps",
number = "1",
volume = "23",
doi = "10.1007/s11051-021-05139-y"
}

Djurišić, I., Dražić, M., Tomović, A., Jovanović, V. P.,& Žikić, R.. (2021). Electrostatically driven energy shift of molecular orbitals of benzene and nicotine in carbon nanotube gaps. in Journal of Nanoparticle Research
Springer, Dordrecht., 23(1).
https://doi.org/10.1007/s11051-021-05139-y

Djurišić I, Dražić M, Tomović A, Jovanović VP, Žikić R. Electrostatically driven energy shift of molecular orbitals of benzene and nicotine in carbon nanotube gaps. in Journal of Nanoparticle Research. 2021;23(1).
doi:10.1007/s11051-021-05139-y .

Djurišić, Ivana, Dražić, Miloš, Tomović, Aleksandar, Jovanović, Vladimir P., Žikić, Radomir, "Electrostatically driven energy shift of molecular orbitals of benzene and nicotine in carbon nanotube gaps" in Journal of Nanoparticle Research, 23, no. 1 (2021),
https://doi.org/10.1007/s11051-021-05139-y . .

TY  - JOUR
AU  - Djurišić, Ivana
AU  - Dražić, Miloš
AU  - Tomović, Aleksandar
AU  - Spasenović, Marko
AU  - Šljivančanin, Zeljko
AU  - Jovanović, Vladimir P.
AU  - Žikić, Radomir
PY  - 2021
UR  - http://rimsi.imsi.bg.ac.rs/handle/123456789/1405
AB  - Functionalization of electrodes is a wide-used strategy in various applications ranging from single-molecule sensing and protein sequencing, to ion trapping, to desalination. We demonstrate, employing non-equilibrium Green ' s function formalism combined with density functional theory, that single-species (N, H, S, Cl, F) termination of graphene nanogap electrodes results in a strong in-gap electrostatic field, induced by species-dependent dipoles formed at the electrode ends. Consequently, the field increases or decreases electronic transport through a molecule (benzene) placed in the nanogap by shifting molecular levels by almost 2 eV in respect to the electrode Fermi level via a field effect akin to the one used for field-effect transistors. We also observed the local gating in graphene nanopores terminated with different single-species atoms. Nitrogen-terminated nanogaps (NtNGs) and nanopores (NtNPs) show the strongest effect. The in-gap potential can be transformed from a plateau-like to a saddle-like shape by tailoring NtNG and NtNP size and termination type. In particular, the saddle-like potential is applicable in single-ion trapping and desalination devices.
PB  - Wiley-V C H Verlag Gmbh, Weinheim
T2  - Chemphyschem
T1  - Field Effect and Local Gating in Nitrogen-Terminated Nanopores (NtNP) and Nanogaps (NtNG) in Graphene
EP  - 341
IS  - 3
SP  - 336
VL  - 22
DO  - 10.1002/cphc.202000771
ER  - 

@article{
author = "Djurišić, Ivana and Dražić, Miloš and Tomović, Aleksandar and Spasenović, Marko and Šljivančanin, Zeljko and Jovanović, Vladimir P. and Žikić, Radomir",
year = "2021",
abstract = "Functionalization of electrodes is a wide-used strategy in various applications ranging from single-molecule sensing and protein sequencing, to ion trapping, to desalination. We demonstrate, employing non-equilibrium Green ' s function formalism combined with density functional theory, that single-species (N, H, S, Cl, F) termination of graphene nanogap electrodes results in a strong in-gap electrostatic field, induced by species-dependent dipoles formed at the electrode ends. Consequently, the field increases or decreases electronic transport through a molecule (benzene) placed in the nanogap by shifting molecular levels by almost 2 eV in respect to the electrode Fermi level via a field effect akin to the one used for field-effect transistors. We also observed the local gating in graphene nanopores terminated with different single-species atoms. Nitrogen-terminated nanogaps (NtNGs) and nanopores (NtNPs) show the strongest effect. The in-gap potential can be transformed from a plateau-like to a saddle-like shape by tailoring NtNG and NtNP size and termination type. In particular, the saddle-like potential is applicable in single-ion trapping and desalination devices.",
publisher = "Wiley-V C H Verlag Gmbh, Weinheim",
journal = "Chemphyschem",
title = "Field Effect and Local Gating in Nitrogen-Terminated Nanopores (NtNP) and Nanogaps (NtNG) in Graphene",
pages = "341-336",
number = "3",
volume = "22",
doi = "10.1002/cphc.202000771"
}

Djurišić, I., Dražić, M., Tomović, A., Spasenović, M., Šljivančanin, Z., Jovanović, V. P.,& Žikić, R.. (2021). Field Effect and Local Gating in Nitrogen-Terminated Nanopores (NtNP) and Nanogaps (NtNG) in Graphene. in Chemphyschem
Wiley-V C H Verlag Gmbh, Weinheim., 22(3), 336-341.
https://doi.org/10.1002/cphc.202000771

Djurišić I, Dražić M, Tomović A, Spasenović M, Šljivančanin Z, Jovanović VP, Žikić R. Field Effect and Local Gating in Nitrogen-Terminated Nanopores (NtNP) and Nanogaps (NtNG) in Graphene. in Chemphyschem. 2021;22(3):336-341.
doi:10.1002/cphc.202000771 .

Djurišić, Ivana, Dražić, Miloš, Tomović, Aleksandar, Spasenović, Marko, Šljivančanin, Zeljko, Jovanović, Vladimir P., Žikić, Radomir, "Field Effect and Local Gating in Nitrogen-Terminated Nanopores (NtNP) and Nanogaps (NtNG) in Graphene" in Chemphyschem, 22, no. 3 (2021):336-341,
https://doi.org/10.1002/cphc.202000771 . .

TY  - JOUR
AU  - Djurišić, Ivana
AU  - Dražić, Miloš
AU  - Tomović, Aleksandar
AU  - Spasenović, Marko
AU  - Sljivancanin, Zeljko
AU  - Jovanović, Vladimir P.
AU  - Žikić, Radomir
PY  - 2020
UR  - http://rimsi.imsi.bg.ac.rs/handle/123456789/1346
AB  - Fast, reliable, and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress in various nanopore-based sequencing configurations, challenges that remain in resolution and chromosome-size-long readout call for new approaches. Here we found strong rectification in the transversal current during single-stranded DNA translocation through a nanopore with side-embedded N-terminated carbon nanotube electrodes. Employing density functional theory and nonequilibrium Green's function formalisms, we show that the rectifying ratio (response to square pulses of alternating bias) bears high nucleobase specificity. Rectification arises because of bias-dependent resistance asymmetry on the deoxyribonucleotide-electrode interfaces. The asymmetry induces molecular charging and highest occupied molecular orbital pinning to the electrochemical potential of one of the electrodes, assisted by an in-gap electric-field effect caused by dipoles at the terminated electrode ends. We propose the rectifying ratio, due to its order-of-magnitude-difference nucleobase selectivity and robustness to electrode-molecule orientation, as a promising readout quantifier for single-base resolution and chromosome-size-long single-read DNA sequencing. The proposed configurations are within experimental reach from the viewpoint of both nanofabrication and small current measurement.
PB  - Amer Chemical Soc, Washington
T2  - Acs Applied Nano Materials
T1  - DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N-Terminated Carbon Nanotube Electrodes
EP  - 3043
IS  - 3
SP  - 3034
VL  - 3
DO  - 10.1021/acsanm.0c00385
ER  - 

@article{
author = "Djurišić, Ivana and Dražić, Miloš and Tomović, Aleksandar and Spasenović, Marko and Sljivancanin, Zeljko and Jovanović, Vladimir P. and Žikić, Radomir",
year = "2020",
abstract = "Fast, reliable, and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress in various nanopore-based sequencing configurations, challenges that remain in resolution and chromosome-size-long readout call for new approaches. Here we found strong rectification in the transversal current during single-stranded DNA translocation through a nanopore with side-embedded N-terminated carbon nanotube electrodes. Employing density functional theory and nonequilibrium Green's function formalisms, we show that the rectifying ratio (response to square pulses of alternating bias) bears high nucleobase specificity. Rectification arises because of bias-dependent resistance asymmetry on the deoxyribonucleotide-electrode interfaces. The asymmetry induces molecular charging and highest occupied molecular orbital pinning to the electrochemical potential of one of the electrodes, assisted by an in-gap electric-field effect caused by dipoles at the terminated electrode ends. We propose the rectifying ratio, due to its order-of-magnitude-difference nucleobase selectivity and robustness to electrode-molecule orientation, as a promising readout quantifier for single-base resolution and chromosome-size-long single-read DNA sequencing. The proposed configurations are within experimental reach from the viewpoint of both nanofabrication and small current measurement.",
publisher = "Amer Chemical Soc, Washington",
journal = "Acs Applied Nano Materials",
title = "DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N-Terminated Carbon Nanotube Electrodes",
pages = "3043-3034",
number = "3",
volume = "3",
doi = "10.1021/acsanm.0c00385"
}

Djurišić, I., Dražić, M., Tomović, A., Spasenović, M., Sljivancanin, Z., Jovanović, V. P.,& Žikić, R.. (2020). DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N-Terminated Carbon Nanotube Electrodes. in Acs Applied Nano Materials
Amer Chemical Soc, Washington., 3(3), 3034-3043.
https://doi.org/10.1021/acsanm.0c00385

Djurišić I, Dražić M, Tomović A, Spasenović M, Sljivancanin Z, Jovanović VP, Žikić R. DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N-Terminated Carbon Nanotube Electrodes. in Acs Applied Nano Materials. 2020;3(3):3034-3043.
doi:10.1021/acsanm.0c00385 .

Djurišić, Ivana, Dražić, Miloš, Tomović, Aleksandar, Spasenović, Marko, Sljivancanin, Zeljko, Jovanović, Vladimir P., Žikić, Radomir, "DNA Sequencing with Single-Stranded DNA Rectification in a Nanogap Gated by N-Terminated Carbon Nanotube Electrodes" in Acs Applied Nano Materials, 3, no. 3 (2020):3034-3043,
https://doi.org/10.1021/acsanm.0c00385 . .