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  • 1.
    Banerjee, Debapriya
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Vovusha, Hakkim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Pang, Yanhong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Oumata, Nassima
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Sanyal, Suparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Spectroscopic and DFT studies on 6-Aminophenanthridine and its derivatives provide insights in their activity towards ribosomal RNA2014In: Biochimie, ISSN 0300-9084, E-ISSN 1638-6183, Vol. 97, p. 194-199Article in journal (Refereed)
    Abstract [en]

    6-Aminophenanthridine (6AP), a plant alkaloid possessing antiprion activity, inhibits ribosomal RNA dependent protein folding activity of the ribosome (referred as PFAR). We have compared 6AP and its three derivatives 6AP8Cl, 6AP8CF3 and 6APi for their activity in inhibition of PFAR. Since PFAR inhibition requires 6AP and its derivatives to bind to the ribosomal RNA (rRNA), we have measured the binding affinity of these molecules to domain V of 23S rRNA using fluorescence spectroscopy. Our results show that similar to the antiprion activity, both the inhibition of PFAR and the affinity towards rRNA follow the order 6AP8CF3 > 6AP8Cl > 6AP, while 6APi is totally inactive. To have a molecular insight for the difference in activity despite similarities in structure, we have calculated the nucleus independent chemical shift using first principles density functional theory. The result suggests that the deviation of planarity in 6APi and steric hindrance from its bulky side chain are the probable reasons which prevent it from interacting with rRNA. Finally, we suggest a probable mode of action of 6AP, 6AP8CF3 and 6AP8Cl towards rRNA.

  • 2.
    Hussain, T.
    et al.
    Univ Western Australia, Sch Mol Sci, Perth, WA 6009, Australia;Univ Queensland, Australian Inst Bioengn & Nanotechnol, Ctr Theoret & Computat Mol Sci, Brisbane, Qld 4072, Australia.
    Vovusha, Hakkim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. KAUST, Phys Sci & Engn Div PSE, Thuwal 239556900, Saudi Arabia.
    Umer, R.
    Univ Southern Queensland, Ctr Future Mat, Toowoomba, Qld 4350, Australia.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Royal Inst Technol KTH, Dept Mat & Engn, Appl Mat Phys, S-10044 Stockholm, Sweden.
    Superior sensing affinities of acetone towards vacancy induced and metallized ZnO monolayers2018In: Applied Surface Science, ISSN 0169-4332, E-ISSN 1873-5584, Vol. 456, p. 711-716Article in journal (Refereed)
    Abstract [en]

    The sensing propensities of acetone molecule towards zinc oxide monolayers (ZnO-ML) have been studied by means of density functional theory (DFT) calculations. Our van der Waals induced first principles calculations revealed that pristine ZnO-ML barely binds acetone, which limits its application as acetone sensing materials. However the formation of vacancies and foreign element doping improves acetone binding drastically. Among several defects, divacancy, and metal doping Li, Sc and Ti functionalization on ZnO-ML has been found the most promising ones. Presence of dangling electrons and partial positive charges in case of vacancy-induced and metallized ZnO-ML respectively, is believed to enhance the binding of acetone on the monolayers. The acetone-ZnO binding behavior has been further explained through studying the electronic properties by density of states and charge transfer mechanism though Bader analysis. Thus defected and metallized ZnO-ML could be a promising nano sensor for efficient sensing/capture of acetone.

  • 3.
    Hussain, Tanveer
    et al.
    Univ Queensland, Australian Inst Bioengn & Nanotechnol, Ctr Theoret & Computat Mol Sci, Australia.
    Kaewmaraya, Thanayut
    Khon Kaen Univ, Dept Phys, Integrated Nanotechnol Res Ctr, Khon Kaen, Thailand; Nanotec KKU Ctr Excellence Adv Nanomat Energy Pro, Khon Kaen, Thailand.
    Chakraborty, Sudip
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Vovusha, Hakkim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. King Abdullah Univ Sci & Technol, Phys Sci & Engn Div PSE, Thuwal, Saudi Arabia.
    Amornkitbamrung, Vittaya
    Khon Kaen Univ, Dept Phys, Integrated Nanotechnol Res Ctr, Khon Kaen, Thailand; Nanotec KKU Ctr Excellence Adv Nanomat Energy Pro, Khon Kaen, Thailand.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Royal Inst Technol KTH, Dept Mat & Engn, Appl Mat Phys, Stockholm, Sweden.
    Defected and Functionalized Germanene-based Nanosensors under Sulfur Comprising Gas Exposure2018In: ACS SENSORS, ISSN 2379-3694, Vol. 3, no 4, p. 867-874Article in journal (Refereed)
    Abstract [en]

    Efficient sensing of sulfur containing toxic gases like H2S and SO2 is of the utmost importance due to the adverse effects of these noxious gases. Absence of an efficient 2D-based nanosensor capable of anchoring H2S and SO2 with feasible binding and an apparent variation in electronic properties upon the exposure of gas molecules has motivated us to explore the promise of a germanene nanosheet (Ge-NS) for this purpose. In the present study, we have performed a comprehensive computational investigation by means of DFT-based first-principles calculations to envisage the structural, electronic, and gas sensing properties of pristine, defected, and metal substituted Ge-NSs. Our initial screening has revealed that although interaction of SO2 with pristine Ge-NSs is within the desirable range, H2S binding however falls below the required values to guarantee an effective sensing. To improve the binding characteristics, we have considered the interactions between H2S and SO2 with defected and metal substituted Ge-NS. The systematic removals of Ge atoms from a reasonably large super cell lead to monovacancy, divacancies, and trivacancies in Ge-NS. Similarly, different transition metals like As, Co, Cu, Fe, Ga, Ge, Ni, and Zn have been substituted into the monolayer to realize substituted Ge-NS. Our van der Waals corrected DFT calculations have concluded that the vacancy and substitution defects not only improve the binding characteristics but also enhance the sensing propensity of both H2S and SO2. The total and projected density of states show significant variations in electronic properties of pristine and defected Ge-NSs before and after the exposure to the gases, which are essential in constituting a signal to be detected by the external circuit of the sensor. We strongly believe that our present work would not only advance the knowledge towards the application of Ge-NS-based sensing but also provide motivation for the synthesis of such efficient nanosensor for H2S and SO2 based on Ge monolayer.

  • 4.
    Hussain, Tanveer
    et al.
    Univ Queensland, Ctr Theoret & Computat Mol Sci, Australian Inst Bioengn & Nanotechnol, Brisbane, Qld 4072, Australia..
    Vovusha, Hakkim
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. KAUST, Phys Sci & Engn Div PSE, Thuwal 239556900, Saudi Arabia.
    Kaewmaraya, Thanayut
    Khon Kaen Univ, Integrated Nanotechnol Res Ctr, Dept Phys, Khon Kaen, Thailand..
    Amornkitbamrung, Vittaya
    Khon Kaen Univ, Integrated Nanotechnol Res Ctr, Dept Phys, Khon Kaen, Thailand.;Nanotec KKU Ctr Excellence Adv Nanomat Energy Pro, Khon Kaen, Thailand..
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Royal Inst Technol KTH, Appl Mat Phys, Dept Mat & Engn, S-10044 Stockholm, Sweden..
    Adsorption characteristics of DNA nucleobases, aromatic amino acids and heterocyclic molecules on silicene and germanene monolayers2018In: Sensors and actuators. B, Chemical, ISSN 0925-4005, E-ISSN 1873-3077, Vol. 255, p. 2713-2720Article in journal (Refereed)
    Abstract [en]

    Binding of DNA/RNA nucleobases, aromatic amino acids and heterocyclic molecules on two-dimensional silicene and germanene sheets have been investigated for the application of sensing of biomolecules using first principle density functional theory calculations. Binding energy range for nucleobases, amino acids and heterocyclic molecules with both the sheets have been found to be (0.43-1.16 eV), (0.70-1.58 eV) and (0.22-0.96 eV) respectively, which along with the binding distances show that these molecules bind to both sheets by physisorption and chemisorption process. The exchange of electric charges between the monolayers and the incident molecules has been examined by means of Bader charge analysis. It has been observed that the introduction of DNA/RNA nucleobases, aromatic amino acids and heterocyclic molecules alters the electronic properties of both silicene and germanene nano sheets as studied by plotting the total (TDOS) and partial (PDOS) density of states. The DOS plots reveal the variation in the band gaps of both silicene and germanene caused by the introduction of studied molecules. Based on the obtained results we suggest that both silicene and germanene monolayers in their pristine form could be useful for sensing of biomolecules.

  • 5.
    Vovusha, Hakkim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. 4700 King Abdullah Univ Sci & Technol, Mat Sci & Engn Program, Thuwal 239556900, Saudi Arabia..
    Amorim, Rodrigo G.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. UFF, Dept Fis, ICEx, R Des Ellis Hermydio Figueira 783, Volta Redonda, RJ, Brazil..
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Controlling the orientation of nucleobases by dipole moment interaction with graphene/h-BN interfaces2018In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 8, no 12, p. 6527-6531Article in journal (Refereed)
    Abstract [en]

    The interfaces in 2D hybrids of graphene and h-BN provide interesting possibilities of adsorbing and manipulating atomic and molecular entities. In this paper, with the aid of density functional theory, we demonstrate the adsorption characteristics of DNA nucleobases at different interfaces of 2D hybrid nanoflakes of graphene and h-BN. The interfaces provide stronger binding to the nucleobases in comparison to pure graphene and h-BN nanoflakes. It is also revealed that the individual dipole moments of the nucleobases and nanoflakes dictate the orientation of the nucleobases at the interfaces of the hybrid structures. The results of our study point towards a possible route to selectively control the orientation of individual molecules in biosensors.

  • 6.
    Vovusha, Hakkim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    DFT and TD-DFT studies on the electronic and optical properties of explosive molecules adsorbed on boron nitride and graphene nano flakes2015In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 5, no 6, p. 4599-4608Article in journal (Refereed)
    Abstract [en]

    The adsorption characteristics of explosive molecules: RDX, TATP, HMTD, TNT, HMX and PETN with boron nitride (BN) and graphene (G) flakes have been investigated using first principles density functional theory (DFT). It has been found that the binding between BN flakes and the explosive molecules is stronger than that with G flakes due to higher charge transfer in the BN-complexes. The energy decomposition analysis indicates that the dispersive interaction is the most dominant one. The optical properties and the nature of electronic transitions of BN and G-explosive complexes are studied by time dependent DFT (TD-DFT). It is observed that the strong interaction with BN flakes quenches the optical spectra by a significant amount whereas the graphene flakes leave the spectra almost unperturbed. Our findings of differential characteristics of 2D flakes will be useful for the designing of nanomaterials for the detection of aromatic and nonaromatic explosive molecules.

  • 7.
    Vovusha, Hakkim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Sanyal, Suparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Sanyal, Biplab
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Interaction of Nucleobases and Aromatic Amino Acids with Graphene Oxide and Graphene Flakes2013In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 4, no 21, p. 3710-3718Article in journal (Refereed)
    Abstract [en]

    In this work, we have studied interactions of nucleobases and aromatic amino acids with graphene (G) and graphene oxide (GO) flakes by ab initio density functional theory (DFT). It is evident from the results that GO complexes are stabilized by hydrogen bonding interactions whereas G complexes are stabilized by pi-pi interactions, leading to enhanced binding energies for GO complexes compared to G complexes. Moreover, time-dependent DFT (TD-DFT) calculations for the optical properties reveal that the GO nanoflakes and GO-nucleobase composite absorb visible light in the range of 400-700 nm, which may be useful for light-emitting devices. The insights obtained from our study will be useful to understand the role of GO flakes as carriers in targeted drug delivery and biosensors.

1 - 7 of 7
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