TY  - JOUR
AU  - Milovanović, Branislav
AU  - Petković, Milena
AU  - Popov, Igor
AU  - Etinski, Mihajlo
PY  - 2021
UR  - http://rimsi.imsi.bg.ac.rs/handle/123456789/1499
AB  - Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation-cation distance in the central ion channel of quadruplexes. In this work, density functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines' carbonyl groups. The reported findings are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications.
PB  - Amer Chemical Soc, Washington
T2  - Journal of Physical Chemistry B
T1  - Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex
EP  - 12005
IS  - 43
SP  - 11996
VL  - 125
DO  - 10.1021/acs.jpcb.1c05598
ER  - 

@article{
author = "Milovanović, Branislav and Petković, Milena and Popov, Igor and Etinski, Mihajlo",
year = "2021",
abstract = "Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation-cation distance in the central ion channel of quadruplexes. In this work, density functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines' carbonyl groups. The reported findings are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications.",
publisher = "Amer Chemical Soc, Washington",
journal = "Journal of Physical Chemistry B",
title = "Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex",
pages = "12005-11996",
number = "43",
volume = "125",
doi = "10.1021/acs.jpcb.1c05598"
}

Milovanović, B., Petković, M., Popov, I.,& Etinski, M.. (2021). Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex. in Journal of Physical Chemistry B
Amer Chemical Soc, Washington., 125(43), 11996-12005.
https://doi.org/10.1021/acs.jpcb.1c05598

Milovanović B, Petković M, Popov I, Etinski M. Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex. in Journal of Physical Chemistry B. 2021;125(43):11996-12005.
doi:10.1021/acs.jpcb.1c05598 .

Milovanović, Branislav, Petković, Milena, Popov, Igor, Etinski, Mihajlo, "Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex" in Journal of Physical Chemistry B, 125, no. 43 (2021):11996-12005,
https://doi.org/10.1021/acs.jpcb.1c05598 . .

TY  - JOUR
AU  - Milovanović, Branislav
AU  - Etinski, Mihajlo
AU  - Popov, Igor
PY  - 2021
UR  - http://rimsi.imsi.bg.ac.rs/handle/123456789/1497
AB  - We are witnessing a change of paradigm from the conventional top-down to the bottom-up fabrication of nanodevices and particularly optoelectronic devices. A promising example of the bottom-up approach is self-assembling of molecules into layers with predictable and reproducible structural, electronic and optical properties. Nucleobases possess extraordinary ability to self-assembly into one-, two-, and three-dimensional structures. Optical properties of nucleotides are not suitable for wider application to optoelectronics and photovoltaics due to their large optical band gap, which is in contrast to rylene-based dyes that have been intensively investigated in organic optoelectronics. However, these lack the self-assembly capability of nucleobases. Combinations of covalently decorated guanine molecules with rylene type chromophores present 'the best of the both worlds'. Due to the large size of such compounds and its flexible nature their self-assemblies have not been fully understood yet. Here, we use a theoretical approach to study the structural, energetic and optical properties of rylene-based dye decorated guanine (GPDI), as self-assembled on a graphene sheet. Particularly we utilize the density-functional based tight-binding method to study atomic structure of these systems including the potential energy surface of GPDI and stability and organization of single- and multilayered GPDIs on graphene sheet. Using density-functional theory (DFT) we employ the energy decomposition analysis to gain a deeper insight into the contributions of different moieties to stability of GPDI films. Using time dependent DFT we analyze optical properties of these systems. We find that atomically thin films consisting of only a few molecular layers with large surface areas are more favorable than isolated thick islands. Our study of excited states indicates existence of charge separated states similar to ones found in the well-studied hydrogen bonded organic frameworks. The self-assembly characterized with a large homogeneous coverage and long-living charge-separated states provide the great potential for optoelectronic applications.
PB  - IOP Publishing Ltd, Bristol
T2  - Nanotechnology
T1  - Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study
IS  - 43
VL  - 32
DO  - 10.1088/1361-6528/ac162c
ER  - 

@article{
author = "Milovanović, Branislav and Etinski, Mihajlo and Popov, Igor",
year = "2021",
abstract = "We are witnessing a change of paradigm from the conventional top-down to the bottom-up fabrication of nanodevices and particularly optoelectronic devices. A promising example of the bottom-up approach is self-assembling of molecules into layers with predictable and reproducible structural, electronic and optical properties. Nucleobases possess extraordinary ability to self-assembly into one-, two-, and three-dimensional structures. Optical properties of nucleotides are not suitable for wider application to optoelectronics and photovoltaics due to their large optical band gap, which is in contrast to rylene-based dyes that have been intensively investigated in organic optoelectronics. However, these lack the self-assembly capability of nucleobases. Combinations of covalently decorated guanine molecules with rylene type chromophores present 'the best of the both worlds'. Due to the large size of such compounds and its flexible nature their self-assemblies have not been fully understood yet. Here, we use a theoretical approach to study the structural, energetic and optical properties of rylene-based dye decorated guanine (GPDI), as self-assembled on a graphene sheet. Particularly we utilize the density-functional based tight-binding method to study atomic structure of these systems including the potential energy surface of GPDI and stability and organization of single- and multilayered GPDIs on graphene sheet. Using density-functional theory (DFT) we employ the energy decomposition analysis to gain a deeper insight into the contributions of different moieties to stability of GPDI films. Using time dependent DFT we analyze optical properties of these systems. We find that atomically thin films consisting of only a few molecular layers with large surface areas are more favorable than isolated thick islands. Our study of excited states indicates existence of charge separated states similar to ones found in the well-studied hydrogen bonded organic frameworks. The self-assembly characterized with a large homogeneous coverage and long-living charge-separated states provide the great potential for optoelectronic applications.",
publisher = "IOP Publishing Ltd, Bristol",
journal = "Nanotechnology",
title = "Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study",
number = "43",
volume = "32",
doi = "10.1088/1361-6528/ac162c"
}

Milovanović, B., Etinski, M.,& Popov, I.. (2021). Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study. in Nanotechnology
IOP Publishing Ltd, Bristol., 32(43).
https://doi.org/10.1088/1361-6528/ac162c

Milovanović B, Etinski M, Popov I. Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study. in Nanotechnology. 2021;32(43).
doi:10.1088/1361-6528/ac162c .

Milovanović, Branislav, Etinski, Mihajlo, Popov, Igor, "Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study" in Nanotechnology, 32, no. 43 (2021),
https://doi.org/10.1088/1361-6528/ac162c . .